Starting phenix.real_space_refine on Wed Feb 14 02:18:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmr_26000/02_2024/7tmr_26000_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmr_26000/02_2024/7tmr_26000.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmr_26000/02_2024/7tmr_26000.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmr_26000/02_2024/7tmr_26000.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmr_26000/02_2024/7tmr_26000_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tmr_26000/02_2024/7tmr_26000_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 1.128 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 231 5.16 5 C 36779 2.51 5 N 9883 2.21 5 O 10900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 117": "OE1" <-> "OE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A GLU 487": "OE1" <-> "OE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C TYR 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C ASP 483": "OD1" <-> "OD2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "D TYR 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 296": "OE1" <-> "OE2" Residue "D TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 434": "OE1" <-> "OE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 289": "OE1" <-> "OE2" Residue "E GLU 366": "OE1" <-> "OE2" Residue "E TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "E ASP 483": "OD1" <-> "OD2" Residue "E GLU 496": "OE1" <-> "OE2" Residue "E GLU 609": "OE1" <-> "OE2" Residue "F GLU 296": "OE1" <-> "OE2" Residue "F ASP 311": "OD1" <-> "OD2" Residue "F GLU 323": "OE1" <-> "OE2" Residue "F GLU 437": "OE1" <-> "OE2" Residue "G TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 145": "OD1" <-> "OD2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 52": "OD1" <-> "OD2" Residue "M PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 196": "OD1" <-> "OD2" Residue "M GLU 198": "OE1" <-> "OE2" Residue "M GLU 199": "OE1" <-> "OE2" Residue "a TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 721": "OE1" <-> "OE2" Residue "a PHE 774": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 213": "OD1" <-> "OD2" Residue "b ASP 248": "OD1" <-> "OD2" Residue "b GLU 255": "OE1" <-> "OE2" Residue "c TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 285": "OE1" <-> "OE2" Residue "d GLU 336": "OE1" <-> "OE2" Residue "f PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 113": "OD1" <-> "OD2" Residue "h GLU 3": "OE1" <-> "OE2" Residue "h PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 157": "OD1" <-> "OD2" Residue "i TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 48": "OD1" <-> "OD2" Residue "i PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 48": "OD1" <-> "OD2" Residue "k PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 3": "OE1" <-> "OE2" Residue "m PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 3": "OE1" <-> "OE2" Residue "o PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 57795 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 4548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4548 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: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 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: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3695 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 448} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 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: 4567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4567 Classifications: {'peptide': 593} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 562} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 3727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3727 Classifications: {'peptide': 478} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 451} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1315 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 449 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 350 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 14, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 23, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 233 Chain: "H" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 556 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 1, 'TRANS': 110} Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 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': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 155 Chain: "I" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1294 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 139} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 475 Unresolved non-hydrogen angles: 590 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 3, 'ASN:plan1': 14, 'ASP:plan': 8, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 252 Chain: "J" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 551 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 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': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 155 Chain: "K" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1477 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 6, 'TRANS': 218} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 404 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 11, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 162 Chain: "L" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 551 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 1, 'TRANS': 109} Unresolved non-hydrogen bonds: 325 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 265 Unresolved non-hydrogen chiralities: 27 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': 15, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 155 Chain: "M" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1439 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 3, 'TRANS': 210} Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 371 Unresolved non-hydrogen dihedrals: 220 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 166 Chain: "N" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 587 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 109} Unresolved non-hydrogen bonds: 352 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 279 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': 6, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 201 Chain: "O" Number of atoms: 1841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 1841 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 307} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 347} Chain breaks: 1 Unresolved non-hydrogen bonds: 1111 Unresolved non-hydrogen angles: 1422 Unresolved non-hydrogen dihedrals: 914 Unresolved non-hydrogen chiralities: 111 Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 6, 'TYR:plan': 13, 'ASN:plan1': 23, 'TRP:plan': 3, 'ASP:plan': 18, 'PHE:plan': 21, 'GLU:plan': 28, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 613 Chain: "P" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 2228 Classifications: {'peptide': 441} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 395} Link IDs: {'PTRANS': 9, 'TRANS': 431} Chain breaks: 2 Unresolved non-hydrogen bonds: 1377 Unresolved non-hydrogen angles: 1757 Unresolved non-hydrogen dihedrals: 1113 Unresolved non-hydrogen chiralities: 153 Planarities with less than four sites: {'GLN:plan1': 24, 'ASP:plan': 29, 'TYR:plan': 11, 'ASN:plan1': 23, 'TRP:plan': 5, 'HIS:plan': 9, 'PHE:plan': 15, 'GLU:plan': 32, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 702 Chain: "a" Number of atoms: 5338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5338 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'PTRANS': 21, 'TRANS': 712} Chain breaks: 2 Unresolved non-hydrogen bonds: 639 Unresolved non-hydrogen angles: 800 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 4, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 18, 'PHE:plan': 8, 'GLU:plan': 17, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 382 Chain: "b" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 400 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "c" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1454 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 195} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "d" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2776 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 333} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "e" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 510 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 60} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "f" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 467 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "g" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1134 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "h" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "i" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "j" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1125 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "k" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "l" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "m" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1137 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "n" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1129 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "o" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1145 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 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: 21.87, per 1000 atoms: 0.38 Number of scatterers: 57795 At special positions: 0 Unit cell: (145.402, 188.662, 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 231 16.00 P 2 15.00 O 10900 8.00 N 9883 7.00 C 36779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.58 Conformation dependent library (CDL) restraints added in 8.1 seconds 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 281 helices and 41 sheets defined 58.9% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.02 Creating SS restraints... Processing helix chain 'A' and resid 112 through 119 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 262 through 271 Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 304 through 307 No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 311 through 314 Processing helix chain 'A' and resid 326 through 346 removed outlier: 4.766A pdb=" N ILE A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 371 Processing helix chain 'A' and resid 384 through 393 Processing helix chain 'A' and resid 426 through 434 Processing helix chain 'A' and resid 443 through 447 Processing helix chain 'A' and resid 466 through 474 removed outlier: 3.609A pdb=" N LYS A 469 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 502 removed outlier: 3.686A pdb=" N GLN A 497 " --> pdb=" O GLU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 506 No H-bonds generated for 'chain 'A' and resid 504 through 506' Processing helix chain 'A' and resid 509 through 524 Processing helix chain 'A' and resid 540 through 562 Processing helix chain 'A' and resid 567 through 586 removed outlier: 5.588A pdb=" N ASP A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LYS A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 591 No H-bonds generated for 'chain 'A' and resid 589 through 591' Processing helix chain 'A' and resid 593 through 614 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 106 through 108 No H-bonds generated for 'chain 'B' and resid 106 through 108' Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 180 through 190 Processing helix chain 'B' and resid 195 through 198 No H-bonds generated for 'chain 'B' and resid 195 through 198' Processing helix chain 'B' and resid 219 through 230 Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 249 through 269 Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 281 through 294 Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 308 through 317 Processing helix chain 'B' and resid 345 through 353 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 383 through 386 No H-bonds generated for 'chain 'B' and resid 383 through 386' Processing helix chain 'B' and resid 396 through 420 removed outlier: 4.543A pdb=" N ALA B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL B 419 " --> pdb=" O ALA B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 427 through 442 Processing helix chain 'B' and resid 454 through 467 removed outlier: 4.686A pdb=" N ILE B 467 " --> pdb=" O SER B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 484 removed outlier: 3.846A pdb=" N GLU B 483 " --> pdb=" O LYS B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 119 Processing helix chain 'C' and resid 238 through 243 Processing helix chain 'C' and resid 263 through 272 Processing helix chain 'C' and resid 287 through 299 Proline residue: C 298 - end of helix Processing helix chain 'C' and resid 311 through 314 Processing helix chain 'C' and resid 326 through 346 removed outlier: 4.502A pdb=" N ILE C 333 " --> pdb=" O ARG C 329 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N TYR C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 371 Processing helix chain 'C' and resid 382 through 393 removed outlier: 3.818A pdb=" N GLY C 385 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 388 " --> pdb=" O GLY C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 434 removed outlier: 3.706A pdb=" N GLY C 433 " --> pdb=" O THR C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 447 Processing helix chain 'C' and resid 462 through 464 No H-bonds generated for 'chain 'C' and resid 462 through 464' Processing helix chain 'C' and resid 466 through 474 removed outlier: 3.636A pdb=" N LYS C 469 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP C 472 " --> pdb=" O LYS C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 499 Processing helix chain 'C' and resid 509 through 524 Processing helix chain 'C' and resid 540 through 562 Processing helix chain 'C' and resid 567 through 573 removed outlier: 3.743A pdb=" N ASP C 572 " --> pdb=" O SER C 568 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 586 removed outlier: 4.591A pdb=" N LYS C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N PHE C 586 " --> pdb=" O SER C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 591 No H-bonds generated for 'chain 'C' and resid 589 through 591' Processing helix chain 'C' and resid 593 through 615 Processing helix chain 'D' and resid 16 through 19 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 141 through 143 No H-bonds generated for 'chain 'D' and resid 141 through 143' Processing helix chain 'D' and resid 156 through 159 No H-bonds generated for 'chain 'D' and resid 156 through 159' Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 219 through 232 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 250 through 268 removed outlier: 4.014A pdb=" N THR D 255 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Proline residue: D 256 - end of helix removed outlier: 3.769A pdb=" N TYR D 268 " --> pdb=" O TYR D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 Processing helix chain 'D' and resid 308 through 317 Processing helix chain 'D' and resid 345 through 353 removed outlier: 3.856A pdb=" N ILE D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 396 through 419 Processing helix chain 'D' and resid 427 through 442 Processing helix chain 'D' and resid 454 through 467 removed outlier: 4.260A pdb=" N ILE D 467 " --> pdb=" O SER D 463 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 472 No H-bonds generated for 'chain 'D' and resid 470 through 472' Processing helix chain 'D' and resid 478 through 484 Processing helix chain 'E' and resid 112 through 119 Processing helix chain 'E' and resid 238 through 242 Processing helix chain 'E' and resid 262 through 272 Processing helix chain 'E' and resid 287 through 299 Proline residue: E 298 - end of helix Processing helix chain 'E' and resid 311 through 314 Processing helix chain 'E' and resid 326 through 345 removed outlier: 3.768A pdb=" N GLU E 330 " --> pdb=" O ALA E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 371 Processing helix chain 'E' and resid 377 through 379 No H-bonds generated for 'chain 'E' and resid 377 through 379' Processing helix chain 'E' and resid 384 through 394 removed outlier: 3.911A pdb=" N ARG E 394 " --> pdb=" O SER E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 421 No H-bonds generated for 'chain 'E' and resid 419 through 421' Processing helix chain 'E' and resid 426 through 432 Processing helix chain 'E' and resid 443 through 448 Processing helix chain 'E' and resid 466 through 474 removed outlier: 3.866A pdb=" N LYS E 469 " --> pdb=" O VAL E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 502 removed outlier: 3.818A pdb=" N VAL E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LEU E 501 " --> pdb=" O GLN E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 524 Processing helix chain 'E' and resid 540 through 562 Processing helix chain 'E' and resid 567 through 573 removed outlier: 3.921A pdb=" N ASP E 572 " --> pdb=" O SER E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 586 removed outlier: 4.410A pdb=" N LYS E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N PHE E 586 " --> pdb=" O SER E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 593 through 615 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 141 through 143 No H-bonds generated for 'chain 'F' and resid 141 through 143' Processing helix chain 'F' and resid 156 through 159 No H-bonds generated for 'chain 'F' and resid 156 through 159' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 219 through 231 Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 250 through 268 removed outlier: 3.896A pdb=" N ILE F 253 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR F 255 " --> pdb=" O ARG F 252 " (cutoff:3.500A) Proline residue: F 256 - end of helix removed outlier: 4.084A pdb=" N TYR F 268 " --> pdb=" O TYR F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 308 through 316 Processing helix chain 'F' and resid 345 through 353 removed outlier: 3.828A pdb=" N THR F 350 " --> pdb=" O ILE F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 366 Processing helix chain 'F' and resid 383 through 386 No H-bonds generated for 'chain 'F' and resid 383 through 386' Processing helix chain 'F' and resid 396 through 420 removed outlier: 3.519A pdb=" N ALA F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL F 419 " --> pdb=" O ALA F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 442 Processing helix chain 'F' and resid 454 through 467 removed outlier: 4.058A pdb=" N ILE F 467 " --> pdb=" O SER F 463 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 472 No H-bonds generated for 'chain 'F' and resid 470 through 472' Processing helix chain 'F' and resid 478 through 484 removed outlier: 3.556A pdb=" N GLU F 483 " --> pdb=" O LYS F 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 112 removed outlier: 4.429A pdb=" N LYS G 31 " --> pdb=" O GLU G 27 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP G 40 " --> pdb=" O GLN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 132 Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 146 through 164 removed outlier: 5.191A pdb=" N ASP G 154 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASP G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 163 " --> pdb=" O GLU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 213 Processing helix chain 'G' and resid 215 through 222 Processing helix chain 'H' and resid 7 through 103 removed outlier: 3.610A pdb=" N GLN H 12 " --> pdb=" O ALA H 8 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS H 15 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY H 66 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU H 67 " --> pdb=" O GLY H 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ASP H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 112 removed outlier: 3.857A pdb=" N GLU I 44 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN I 57 " --> pdb=" O ASN I 53 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU I 96 " --> pdb=" O ARG I 92 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASP I 97 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 131 Proline residue: I 119 - end of helix removed outlier: 3.789A pdb=" N LYS I 131 " --> pdb=" O GLU I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 163 removed outlier: 3.507A pdb=" N MET I 152 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP I 154 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP I 155 " --> pdb=" O SER I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 222 removed outlier: 3.945A pdb=" N GLU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU I 213 " --> pdb=" O LEU I 209 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU I 215 " --> pdb=" O SER I 211 " (cutoff:3.500A) Proline residue: I 216 - end of helix Processing helix chain 'J' and resid 3 through 103 removed outlier: 3.718A pdb=" N LYS J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS J 41 " --> pdb=" O THR J 37 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU J 42 " --> pdb=" O ASP J 38 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL J 65 " --> pdb=" O ASN J 61 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLY J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU J 82 " --> pdb=" O GLY J 78 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASP J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASP J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 112 removed outlier: 4.714A pdb=" N ASN K 57 " --> pdb=" O ASN K 53 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE K 58 " --> pdb=" O GLU K 54 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN K 112 " --> pdb=" O SER K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 132 Proline residue: K 119 - end of helix Processing helix chain 'K' and resid 143 through 163 removed outlier: 3.706A pdb=" N VAL K 146 " --> pdb=" O GLU K 143 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASP K 147 " --> pdb=" O ARG K 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS K 153 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASP K 154 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS K 163 " --> pdb=" O TYR K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 213 Processing helix chain 'K' and resid 215 through 223 Processing helix chain 'L' and resid 3 through 102 removed outlier: 4.457A pdb=" N GLY L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLU L 67 " --> pdb=" O GLY L 63 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU L 79 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASP L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ASP L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 75 removed outlier: 3.698A pdb=" N GLY M 58 " --> pdb=" O LYS M 54 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG M 59 " --> pdb=" O GLN M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 85 Processing helix chain 'M' and resid 101 through 103 No H-bonds generated for 'chain 'M' and resid 101 through 103' Processing helix chain 'M' and resid 126 through 171 Processing helix chain 'M' and resid 173 through 214 Proline residue: M 179 - end of helix removed outlier: 4.124A pdb=" N SER M 190 " --> pdb=" O ALA M 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 15 through 24 Processing helix chain 'N' and resid 47 through 58 Processing helix chain 'N' and resid 72 through 74 No H-bonds generated for 'chain 'N' and resid 72 through 74' Processing helix chain 'N' and resid 77 through 85 removed outlier: 3.665A pdb=" N THR N 85 " --> pdb=" O VAL N 81 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 105 No H-bonds generated for 'chain 'N' and resid 103 through 105' Processing helix chain 'N' and resid 107 through 115 Processing helix chain 'O' and resid 30 through 40 Processing helix chain 'O' and resid 58 through 88 Processing helix chain 'O' and resid 107 through 111 Processing helix chain 'O' and resid 127 through 165 Processing helix chain 'O' and resid 175 through 177 No H-bonds generated for 'chain 'O' and resid 175 through 177' Processing helix chain 'O' and resid 203 through 213 Processing helix chain 'O' and resid 243 through 252 Processing helix chain 'O' and resid 264 through 317 removed outlier: 4.062A pdb=" N LEU O 288 " --> pdb=" O LEU O 284 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N VAL O 289 " --> pdb=" O ARG O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 337 through 347 Processing helix chain 'P' and resid 13 through 22 Processing helix chain 'P' and resid 25 through 27 No H-bonds generated for 'chain 'P' and resid 25 through 27' Processing helix chain 'P' and resid 29 through 32 No H-bonds generated for 'chain 'P' and resid 29 through 32' Processing helix chain 'P' and resid 38 through 48 removed outlier: 3.541A pdb=" N ALA P 46 " --> pdb=" O SER P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 77 through 86 Processing helix chain 'P' and resid 90 through 105 Processing helix chain 'P' and resid 107 through 118 removed outlier: 4.745A pdb=" N ASP P 111 " --> pdb=" O ASP P 107 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP P 112 " --> pdb=" O LYS P 108 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE P 117 " --> pdb=" O THR P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 130 Processing helix chain 'P' and resid 136 through 150 Processing helix chain 'P' and resid 158 through 166 Processing helix chain 'P' and resid 168 through 175 Processing helix chain 'P' and resid 180 through 193 Processing helix chain 'P' and resid 197 through 221 removed outlier: 4.487A pdb=" N ASP P 201 " --> pdb=" O GLU P 198 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL P 202 " --> pdb=" O TYR P 199 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS P 208 " --> pdb=" O LEU P 205 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N MET P 211 " --> pdb=" O LYS P 208 " (cutoff:3.500A) Proline residue: P 212 - end of helix removed outlier: 3.555A pdb=" N PHE P 215 " --> pdb=" O PRO P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 255 removed outlier: 3.845A pdb=" N PHE P 255 " --> pdb=" O TRP P 251 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 266 Processing helix chain 'P' and resid 268 through 280 removed outlier: 4.142A pdb=" N LEU P 275 " --> pdb=" O PHE P 271 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS P 276 " --> pdb=" O LEU P 272 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 297 Processing helix chain 'P' and resid 308 through 316 Processing helix chain 'P' and resid 318 through 327 Processing helix chain 'P' and resid 333 through 354 Processing helix chain 'P' and resid 356 through 364 Processing helix chain 'P' and resid 372 through 374 No H-bonds generated for 'chain 'P' and resid 372 through 374' Processing helix chain 'P' and resid 381 through 408 removed outlier: 3.684A pdb=" N LYS P 389 " --> pdb=" O ASP P 385 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ASP P 390 " --> pdb=" O GLU P 386 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASN P 391 " --> pdb=" O PHE P 387 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ILE P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE P 395 " --> pdb=" O ASN P 391 " (cutoff:3.500A) Processing helix chain 'P' and resid 414 through 433 Processing helix chain 'P' and resid 435 through 443 Processing helix chain 'P' and resid 446 through 455 removed outlier: 3.965A pdb=" N ASN P 455 " --> pdb=" O MET P 451 " (cutoff:3.500A) Processing helix chain 'P' and resid 459 through 474 removed outlier: 3.627A pdb=" N GLU P 464 " --> pdb=" O ARG P 460 " (cutoff:3.500A) Processing helix chain 'a' and resid 26 through 36 Processing helix chain 'a' and resid 50 through 52 No H-bonds generated for 'chain 'a' and resid 50 through 52' Processing helix chain 'a' and resid 56 through 78 Processing helix chain 'a' and resid 86 through 96 removed outlier: 3.534A pdb=" N LYS a 90 " --> pdb=" O GLY a 86 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR a 91 " --> pdb=" O ASP a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 141 removed outlier: 3.608A pdb=" N GLN a 140 " --> pdb=" O ASN a 136 " (cutoff:3.500A) Processing helix chain 'a' and resid 196 through 206 Processing helix chain 'a' and resid 243 through 256 Processing helix chain 'a' and resid 267 through 325 removed outlier: 3.787A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 343 through 359 removed outlier: 5.795A pdb=" N ALA a 347 " --> pdb=" O ASP a 344 " (cutoff:3.500A) Processing helix chain 'a' and resid 385 through 395 removed outlier: 4.796A pdb=" N GLY a 389 " --> pdb=" O LYS a 385 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE a 390 " --> pdb=" O PHE a 386 " (cutoff:3.500A) Processing helix chain 'a' and resid 408 through 421 removed outlier: 4.030A pdb=" N ILE a 412 " --> pdb=" O GLY a 408 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Proline residue: a 416 - end of helix Processing helix chain 'a' and resid 426 through 438 Processing helix chain 'a' and resid 443 through 447 Processing helix chain 'a' and resid 456 through 460 Processing helix chain 'a' and resid 464 through 478 Processing helix chain 'a' and resid 520 through 522 No H-bonds generated for 'chain 'a' and resid 520 through 522' Processing helix chain 'a' and resid 526 through 561 removed outlier: 4.600A pdb=" N LEU a 530 " --> pdb=" O GLU a 526 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 595 removed outlier: 3.684A pdb=" N ILE a 569 " --> pdb=" O MET a 565 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE a 573 " --> pdb=" O ILE a 569 " (cutoff:3.500A) Proline residue: a 574 - end of helix removed outlier: 4.297A pdb=" N TYR a 585 " --> pdb=" O GLY a 581 " (cutoff:3.500A) Processing helix chain 'a' and resid 598 through 601 No H-bonds generated for 'chain 'a' and resid 598 through 601' Processing helix chain 'a' and resid 608 through 617 removed outlier: 4.770A pdb=" N MET a 615 " --> pdb=" O MET a 611 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N PHE a 616 " --> pdb=" O LEU a 612 " (cutoff:3.500A) Processing helix chain 'a' and resid 630 through 650 removed outlier: 3.838A 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 712 through 758 removed outlier: 4.323A pdb=" N LEU a 734 " --> pdb=" O THR a 730 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG a 735 " --> pdb=" O ALA a 731 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU a 736 " --> pdb=" O SER a 732 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TRP a 737 " --> pdb=" O TYR a 733 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN a 756 " --> pdb=" O THR a 752 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ILE a 757 " --> pdb=" O MET a 753 " (cutoff:3.500A) Processing helix chain 'a' and resid 764 through 783 removed outlier: 3.958A pdb=" N PHE a 768 " --> pdb=" O PHE a 764 " (cutoff:3.500A) Processing helix chain 'a' and resid 785 through 802 removed outlier: 3.766A pdb=" N GLY a 790 " --> pdb=" O VAL a 786 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS a 801 " --> pdb=" O SER a 797 " (cutoff:3.500A) Processing helix chain 'a' and resid 806 through 809 No H-bonds generated for 'chain 'a' and resid 806 through 809' Processing helix chain 'b' and resid 221 through 244 Processing helix chain 'b' and resid 251 through 253 No H-bonds generated for 'chain 'b' and resid 251 through 253' Processing helix chain 'c' and resid 17 through 39 Processing helix chain 'c' and resid 42 through 44 No H-bonds generated for 'chain 'c' and resid 42 through 44' Processing helix chain 'c' and resid 47 through 53 Processing helix chain 'c' and resid 56 through 90 removed outlier: 3.778A pdb=" N SER c 85 " --> pdb=" O ILE c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 94 through 124 removed outlier: 3.639A pdb=" N THR c 97 " --> pdb=" O PRO c 94 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N THR c 98 " --> pdb=" O ARG c 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU c 101 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE c 102 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL c 109 " --> pdb=" O PHE c 106 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL c 110 " --> pdb=" O CYS c 107 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER c 122 " --> pdb=" O ILE c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 132 through 134 No H-bonds generated for 'chain 'c' and resid 132 through 134' Processing helix chain 'c' and resid 136 through 176 removed outlier: 3.653A pdb=" N ALA c 176 " --> pdb=" O ILE c 172 " (cutoff:3.500A) Processing helix chain 'c' and resid 178 through 207 removed outlier: 4.657A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU c 188 " --> pdb=" O ILE c 184 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLY c 195 " --> pdb=" O GLY c 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 23 removed outlier: 3.893A pdb=" N ASN d 7 " --> pdb=" O VAL d 4 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP d 9 " --> pdb=" O PHE d 6 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ASN d 10 " --> pdb=" O ASN d 7 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLY d 11 " --> pdb=" O ILE d 8 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N PHE d 12 " --> pdb=" O ASP d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 34 Processing helix chain 'd' and resid 39 through 47 Processing helix chain 'd' and resid 52 through 55 removed outlier: 4.619A pdb=" N LEU d 55 " --> pdb=" O GLY d 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 52 through 55' Processing helix chain 'd' and resid 65 through 85 Processing helix chain 'd' and resid 90 through 111 removed outlier: 3.704A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP d 105 " --> pdb=" O GLY d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 122 through 126 Processing helix chain 'd' and resid 129 through 131 No H-bonds generated for 'chain 'd' and resid 129 through 131' Processing helix chain 'd' and resid 136 through 141 removed outlier: 3.619A pdb=" N VAL d 141 " --> pdb=" O PRO d 137 " (cutoff:3.500A) Processing helix chain 'd' and resid 145 through 153 Processing helix chain 'd' and resid 159 through 165 removed outlier: 3.540A pdb=" N CYS d 165 " --> pdb=" O TYR d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 172 No H-bonds generated for 'chain 'd' and resid 170 through 172' Processing helix chain 'd' and resid 180 through 198 Processing helix chain 'd' and resid 204 through 229 removed outlier: 4.300A pdb=" N LEU d 211 " --> pdb=" O CYS d 207 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLN d 229 " --> pdb=" O LEU d 225 " (cutoff:3.500A) Processing helix chain 'd' and resid 235 through 241 Processing helix chain 'd' and resid 251 through 258 removed outlier: 4.252A pdb=" N HIS d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) Processing helix chain 'd' and resid 262 through 269 Processing helix chain 'd' and resid 273 through 275 No H-bonds generated for 'chain 'd' and resid 273 through 275' Processing helix chain 'd' and resid 284 through 301 Processing helix chain 'd' and resid 306 through 331 Processing helix chain 'd' and resid 335 through 340 removed outlier: 5.394A pdb=" N ASN d 339 " --> pdb=" O GLU d 336 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASN d 340 " --> pdb=" O ARG d 337 " (cutoff:3.500A) Processing helix chain 'e' and resid 5 through 23 removed outlier: 3.605A pdb=" N ILE e 23 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 56 Processing helix chain 'f' and resid 12 through 32 removed outlier: 3.773A pdb=" N LEU f 16 " --> pdb=" O CYS f 12 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL f 22 " --> pdb=" O ALA f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 48 through 72 removed outlier: 4.166A pdb=" N GLN f 72 " --> pdb=" O PHE f 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 7 through 43 Proline residue: g 10 - end of helix removed outlier: 3.578A pdb=" N ILE g 15 " --> pdb=" O PHE g 12 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N PHE g 23 " --> pdb=" O ALA g 20 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR g 24 " --> pdb=" O ILE g 21 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N CYS g 43 " --> pdb=" O CYS g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 49 No H-bonds generated for 'chain 'g' and resid 47 through 49' Processing helix chain 'g' and resid 55 through 76 Processing helix chain 'g' and resid 84 through 119 Processing helix chain 'g' and resid 123 through 153 removed outlier: 3.692A pdb=" N PHE g 126 " --> pdb=" O PRO g 123 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL g 127 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL g 138 " --> pdb=" O PHE g 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 42 removed outlier: 5.013A pdb=" N PHE h 23 " --> pdb=" O ALA h 20 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR h 24 " --> pdb=" O ILE h 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS h 34 " --> pdb=" O GLY h 31 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER h 35 " --> pdb=" O THR h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 47 through 49 No H-bonds generated for 'chain 'h' and resid 47 through 49' Processing helix chain 'h' and resid 55 through 77 removed outlier: 4.153A pdb=" N SER h 77 " --> pdb=" O LEU h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 119 Processing helix chain 'h' and resid 123 through 154 removed outlier: 3.846A pdb=" N VAL h 127 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL h 138 " --> pdb=" O PHE h 135 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 5 No H-bonds generated for 'chain 'i' and resid 3 through 5' Processing helix chain 'i' and resid 7 through 42 Proline residue: i 10 - end of helix removed outlier: 3.548A pdb=" N ILE i 15 " --> pdb=" O PHE i 12 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE i 23 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR i 24 " --> pdb=" O ILE i 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS i 34 " --> pdb=" O GLY i 31 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER i 35 " --> pdb=" O THR i 32 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS i 40 " --> pdb=" O VAL i 37 " (cutoff:3.500A) Processing helix chain 'i' and resid 47 through 49 No H-bonds generated for 'chain 'i' and resid 47 through 49' Processing helix chain 'i' and resid 53 through 77 Proline residue: i 56 - end of helix removed outlier: 3.608A pdb=" N TYR i 76 " --> pdb=" O LEU i 73 " (cutoff:3.500A) Processing helix chain 'i' and resid 84 through 121 removed outlier: 4.206A pdb=" N ARG i 117 " --> pdb=" O ASP i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 123 through 155 removed outlier: 3.644A pdb=" N VAL i 127 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL i 138 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR i 155 " --> pdb=" O SER i 152 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 42 removed outlier: 3.928A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 47 through 77 removed outlier: 4.591A pdb=" N PHE j 51 " --> pdb=" O ASP j 48 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL j 55 " --> pdb=" O LYS j 52 " (cutoff:3.500A) Proline residue: j 56 - end of helix removed outlier: 3.588A pdb=" N MET j 59 " --> pdb=" O PRO j 56 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE j 62 " --> pdb=" O MET j 59 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TYR j 76 " --> pdb=" O LEU j 73 " (cutoff:3.500A) Processing helix chain 'j' and resid 84 through 121 removed outlier: 3.977A pdb=" N GLN j 121 " --> pdb=" O ARG j 117 " (cutoff:3.500A) Processing helix chain 'j' and resid 123 through 155 removed outlier: 3.704A pdb=" N VAL j 127 " --> pdb=" O ARG j 124 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL j 138 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR j 155 " --> pdb=" O SER j 152 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 43 Proline residue: k 10 - end of helix removed outlier: 3.543A pdb=" N ILE k 15 " --> pdb=" O PHE k 12 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA k 20 " --> pdb=" O CYS k 17 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE k 22 " --> pdb=" O SER k 19 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR k 24 " --> pdb=" O ILE k 21 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS k 34 " --> pdb=" O GLY k 31 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER k 35 " --> pdb=" O THR k 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 77 removed outlier: 4.511A pdb=" N PHE k 51 " --> pdb=" O ASP k 48 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASN k 53 " --> pdb=" O LEU k 50 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE k 54 " --> pdb=" O PHE k 51 " (cutoff:3.500A) Proline residue: k 56 - end of helix removed outlier: 3.540A pdb=" N CYS k 75 " --> pdb=" O VAL k 72 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR k 76 " --> pdb=" O LEU k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 84 through 120 removed outlier: 3.682A pdb=" N SER k 100 " --> pdb=" O SER k 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER k 120 " --> pdb=" O VAL k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 123 through 155 removed outlier: 3.787A pdb=" N VAL k 127 " --> pdb=" O ARG k 124 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL k 138 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR k 155 " --> pdb=" O SER k 152 " (cutoff:3.500A) Processing helix chain 'l' and resid 7 through 42 Proline residue: l 10 - end of helix removed outlier: 3.559A pdb=" N ALA l 20 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N PHE l 23 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR l 24 " --> pdb=" O ILE l 21 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR l 42 " --> pdb=" O ILE l 39 " (cutoff:3.500A) Processing helix chain 'l' and resid 47 through 49 No H-bonds generated for 'chain 'l' and resid 47 through 49' Processing helix chain 'l' and resid 52 through 77 removed outlier: 3.704A pdb=" N VAL l 55 " --> pdb=" O LYS l 52 " (cutoff:3.500A) Proline residue: l 56 - end of helix Processing helix chain 'l' and resid 84 through 121 removed outlier: 4.443A pdb=" N GLN l 121 " --> pdb=" O ARG l 117 " (cutoff:3.500A) Processing helix chain 'l' and resid 123 through 155 removed outlier: 3.845A pdb=" N VAL l 127 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL l 138 " --> pdb=" O PHE l 135 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR l 155 " --> pdb=" O SER l 152 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 42 removed outlier: 3.665A pdb=" N ALA m 20 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N PHE m 23 " --> pdb=" O ALA m 20 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR m 24 " --> pdb=" O ILE m 21 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER m 35 " --> pdb=" O THR m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 47 through 49 No H-bonds generated for 'chain 'm' and resid 47 through 49' Processing helix chain 'm' and resid 52 through 77 removed outlier: 3.822A pdb=" N VAL m 55 " --> pdb=" O LYS m 52 " (cutoff:3.500A) Proline residue: m 56 - end of helix Processing helix chain 'm' and resid 84 through 121 removed outlier: 4.118A pdb=" N GLN m 121 " --> pdb=" O ARG m 117 " (cutoff:3.500A) Processing helix chain 'm' and resid 124 through 155 removed outlier: 3.589A pdb=" N VAL m 127 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR m 155 " --> pdb=" O SER m 152 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 42 removed outlier: 4.025A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE n 21 " --> pdb=" O CYS n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 47 through 77 removed outlier: 3.509A pdb=" N LEU n 50 " --> pdb=" O PRO n 47 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N PHE n 51 " --> pdb=" O ASP n 48 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE n 54 " --> pdb=" O PHE n 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL n 55 " --> pdb=" O LYS n 52 " (cutoff:3.500A) Proline residue: n 56 - end of helix Processing helix chain 'n' and resid 84 through 121 removed outlier: 4.132A pdb=" N SER n 120 " --> pdb=" O VAL n 116 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN n 121 " --> pdb=" O ARG n 117 " (cutoff:3.500A) Processing helix chain 'n' and resid 123 through 155 removed outlier: 3.541A pdb=" N VAL n 127 " --> pdb=" O ARG n 124 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL n 138 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR n 155 " --> pdb=" O SER n 152 " (cutoff:3.500A) Processing helix chain 'o' and resid 15 through 49 Processing helix chain 'o' and resid 53 through 83 removed outlier: 4.619A pdb=" N MET o 57 " --> pdb=" O GLU o 54 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE o 61 " --> pdb=" O LYS o 58 " (cutoff:3.500A) Proline residue: o 62 - end of helix removed outlier: 4.381A pdb=" N GLY o 82 " --> pdb=" O LEU o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 92 through 127 Processing helix chain 'o' and resid 131 through 163 removed outlier: 3.828A pdb=" N VAL o 135 " --> pdb=" O ARG o 132 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU o 147 " --> pdb=" O SER o 144 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER o 163 " --> pdb=" O THR o 160 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 26 through 31 removed outlier: 3.603A pdb=" N ALA A 26 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 36 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL A 30 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N GLN A 71 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL A 60 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 93 through 97 Processing sheet with id= C, first strand: chain 'A' and resid 189 through 191 Processing sheet with id= D, first strand: chain 'A' and resid 437 through 439 removed outlier: 8.507A pdb=" N THR A 252 " --> pdb=" O VAL A 410 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE A 412 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE A 254 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 414 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ALA A 277 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE A 353 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 279 " --> pdb=" O ILE A 353 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 181 through 185 removed outlier: 6.289A pdb=" N GLU A 199 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE A 185 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ILE A 197 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N PHE A 209 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLU A 199 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N SER A 207 " --> pdb=" O GLU A 199 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLU A 201 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 223 through 226 removed outlier: 6.522A pdb=" N VAL A 399 " --> pdb=" O THR A 224 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 31 through 35 removed outlier: 7.196A pdb=" N ILE B 40 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL B 34 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 75 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE B 76 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU B 69 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLN B 78 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL B 67 " --> pdb=" O GLN B 78 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 101 through 104 Processing sheet with id= I, first strand: chain 'B' and resid 357 through 359 Processing sheet with id= J, first strand: chain 'B' and resid 238 through 241 removed outlier: 8.679A pdb=" N SER B 239 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE B 210 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE B 241 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N PHE B 212 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS B 273 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 211 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU B 275 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA B 213 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE B 277 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N SER B 328 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR B 276 " --> pdb=" O SER B 328 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N THR B 330 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU B 278 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 332 " --> pdb=" O LEU B 278 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 26 through 31 removed outlier: 6.871A pdb=" N ILE C 36 " --> pdb=" O TYR C 28 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N VAL C 30 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL C 34 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN C 71 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL C 60 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU C 47 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS C 90 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N LYS C 50 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N THR C 88 " --> pdb=" O LYS C 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 93 through 97 Processing sheet with id= M, first strand: chain 'C' and resid 189 through 191 removed outlier: 4.614A pdb=" N GLN C 140 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE C 172 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N SER C 160 " --> pdb=" O HIS C 170 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N HIS C 170 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 205 through 209 removed outlier: 6.109A pdb=" N GLU C 201 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE C 182 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 252 through 254 removed outlier: 6.688A pdb=" N ALA C 277 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE C 353 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE C 279 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ASP C 355 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL C 281 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 301 through 303 Processing sheet with id= Q, first strand: chain 'C' and resid 396 through 399 removed outlier: 3.759A pdb=" N VAL C 410 " --> pdb=" O GLY C 396 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 26 through 28 removed outlier: 4.310A pdb=" N LEU D 26 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE D 76 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE D 70 " --> pdb=" O ARG D 74 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ARG D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 101 through 104 removed outlier: 3.562A pdb=" N ASP D 130 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 112 through 114 removed outlier: 7.864A pdb=" N PHE D 113 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU D 240 " --> pdb=" O PHE D 113 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ILE D 210 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N PHE D 241 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N PHE D 212 " --> pdb=" O PHE D 241 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN D 243 " --> pdb=" O PHE D 212 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA D 214 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER D 328 " --> pdb=" O VAL D 274 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR D 276 " --> pdb=" O SER D 328 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N THR D 330 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU D 278 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ILE D 332 " --> pdb=" O LEU D 278 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 357 through 359 removed outlier: 3.596A pdb=" N LEU D 335 " --> pdb=" O ILE D 172 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 26 through 31 removed outlier: 7.192A pdb=" N ILE E 36 " --> pdb=" O TYR E 28 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL E 30 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL E 34 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N GLN E 71 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N VAL E 60 " --> pdb=" O GLN E 71 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 93 through 96 Processing sheet with id= X, first strand: chain 'E' and resid 189 through 192 Processing sheet with id= Y, first strand: chain 'E' and resid 252 through 254 removed outlier: 6.315A pdb=" N MET E 352 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ALA E 415 " --> pdb=" O MET E 352 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA E 354 " --> pdb=" O ALA E 415 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 181 through 185 removed outlier: 6.564A pdb=" N GLU E 199 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE E 185 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE E 197 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE E 209 " --> pdb=" O ILE E 197 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLU E 199 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER E 207 " --> pdb=" O GLU E 199 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU E 201 " --> pdb=" O LYS E 205 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LYS E 205 " --> pdb=" O GLU E 201 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 223 through 226 removed outlier: 6.710A pdb=" N VAL E 399 " --> pdb=" O THR E 224 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 26 through 28 removed outlier: 3.983A pdb=" N LEU F 26 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE F 76 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE F 70 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG F 74 " --> pdb=" O ILE F 70 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLY F 33 " --> pdb=" O ILE F 40 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 101 through 104 Processing sheet with id= AD, first strand: chain 'F' and resid 112 through 114 removed outlier: 7.904A pdb=" N PHE F 113 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU F 240 " --> pdb=" O PHE F 113 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE F 210 " --> pdb=" O SER F 239 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N PHE F 241 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE F 212 " --> pdb=" O PHE F 241 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N SER F 328 " --> pdb=" O VAL F 274 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR F 276 " --> pdb=" O SER F 328 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N THR F 330 " --> pdb=" O THR F 276 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU F 278 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE F 332 " --> pdb=" O LEU F 278 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 357 through 359 Processing sheet with id= AF, first strand: chain 'G' and resid 171 through 174 removed outlier: 3.691A pdb=" N ALA G 137 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 173 " --> pdb=" O ALA G 137 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 171 through 174 removed outlier: 3.528A pdb=" N VAL I 173 " --> pdb=" O ALA I 137 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'K' and resid 171 through 175 Processing sheet with id= AI, first strand: chain 'M' and resid 92 through 98 Processing sheet with id= AJ, first strand: chain 'N' and resid 9 through 11 removed outlier: 3.782A pdb=" N ILE N 11 " --> pdb=" O PHE N 38 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 65 through 68 Processing sheet with id= AL, first strand: chain 'O' and resid 387 through 391 removed outlier: 3.672A pdb=" N ILE O 14 " --> pdb=" O LYS O 328 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'O' and resid 195 through 197 Processing sheet with id= AN, first strand: chain 'a' and resid 335 through 342 removed outlier: 4.083A pdb=" N LEU a 335 " --> pdb=" O ILE a 21 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N GLN a 369 " --> pdb=" O GLN a 18 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'a' and resid 494 through 496 removed outlier: 3.585A pdb=" N LYS a 495 " --> pdb=" O THR a 509 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR a 509 " --> pdb=" O LYS a 495 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO 3745 hydrogen bonds defined for protein. 8988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.04 Time building geometry restraints manager: 19.26 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: 12424 1.33 - 1.45: 12497 1.45 - 1.57: 33487 1.57 - 1.70: 3 1.70 - 1.82: 375 Bond restraints: 58786 Sorted by residual: bond pdb=" CA ASN F 243 " pdb=" C ASN F 243 " ideal model delta sigma weight residual 1.522 1.492 0.030 1.20e-02 6.94e+03 6.36e+00 bond pdb=" CA LEU F 244 " pdb=" C LEU F 244 " ideal model delta sigma weight residual 1.527 1.498 0.030 1.42e-02 4.96e+03 4.35e+00 bond pdb=" CG1 ILE k 22 " pdb=" CD1 ILE k 22 " ideal model delta sigma weight residual 1.513 1.433 0.080 3.90e-02 6.57e+02 4.17e+00 bond pdb=" CA TYR d 97 " pdb=" C TYR d 97 " ideal model delta sigma weight residual 1.523 1.499 0.025 1.30e-02 5.92e+03 3.55e+00 bond pdb=" CA LEU F 242 " pdb=" C LEU F 242 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.27e-02 6.20e+03 3.53e+00 ... (remaining 58781 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.15: 1055 105.15 - 112.83: 31834 112.83 - 120.50: 24813 120.50 - 128.17: 22205 128.17 - 135.84: 264 Bond angle restraints: 80171 Sorted by residual: angle pdb=" N ASN F 243 " pdb=" CA ASN F 243 " pdb=" C ASN F 243 " ideal model delta sigma weight residual 109.07 98.34 10.73 1.61e+00 3.86e-01 4.44e+01 angle pdb=" C THR F 392 " pdb=" CA THR F 392 " pdb=" CB THR F 392 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 angle pdb=" N ILE b 214 " pdb=" CA ILE b 214 " pdb=" C ILE b 214 " ideal model delta sigma weight residual 107.98 115.40 -7.42 1.51e+00 4.39e-01 2.41e+01 angle pdb=" N LEU n 84 " pdb=" CA LEU n 84 " pdb=" C LEU n 84 " ideal model delta sigma weight residual 111.28 106.06 5.22 1.09e+00 8.42e-01 2.29e+01 angle pdb=" C GLU d 202 " pdb=" N PRO d 203 " pdb=" CD PRO d 203 " ideal model delta sigma weight residual 120.60 110.26 10.34 2.20e+00 2.07e-01 2.21e+01 ... (remaining 80166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 34199 30.70 - 61.40: 697 61.40 - 92.10: 67 92.10 - 122.80: 1 122.80 - 153.50: 1 Dihedral angle restraints: 34965 sinusoidal: 11323 harmonic: 23642 Sorted by residual: 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 93.50 -153.50 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" CA MET j 59 " pdb=" C MET j 59 " pdb=" N ALA j 60 " pdb=" CA ALA j 60 " ideal model delta harmonic sigma weight residual 180.00 153.12 26.88 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" O2A ADP E 701 " pdb=" O3A ADP E 701 " pdb=" PA ADP E 701 " pdb=" PB ADP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 -160.52 100.53 1 2.00e+01 2.50e-03 2.84e+01 ... (remaining 34962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 7737 0.054 - 0.108: 1622 0.108 - 0.162: 200 0.162 - 0.216: 9 0.216 - 0.270: 5 Chirality restraints: 9573 Sorted by residual: chirality pdb=" CB ILE m 22 " pdb=" CA ILE m 22 " pdb=" CG1 ILE m 22 " pdb=" CG2 ILE m 22 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU m 68 " pdb=" CB LEU m 68 " pdb=" CD1 LEU m 68 " pdb=" CD2 LEU m 68 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CG LEU o 29 " pdb=" CB LEU o 29 " pdb=" CD1 LEU o 29 " pdb=" CD2 LEU o 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 9570 not shown) Planarity restraints: 10454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR d 249 " 0.069 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO d 250 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO d 250 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO d 250 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 371 " 0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO P 372 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO P 372 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO P 372 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU d 202 " -0.049 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO d 203 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO d 203 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO d 203 " -0.034 5.00e-02 4.00e+02 ... (remaining 10451 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 1039 2.68 - 3.23: 62123 3.23 - 3.79: 96941 3.79 - 4.34: 122492 4.34 - 4.90: 201673 Nonbonded interactions: 484268 Sorted by model distance: nonbonded pdb=" OD1 ASP B 114 " pdb=" N GLY B 115 " model vdw 2.124 2.520 nonbonded pdb=" OG SER m 120 " pdb=" OE1 GLN m 121 " model vdw 2.135 2.440 nonbonded pdb=" OD1 ASP D 87 " pdb=" OG1 THR D 91 " model vdw 2.203 2.440 nonbonded pdb=" O LEU a 323 " pdb=" OG SER a 326 " model vdw 2.205 2.440 nonbonded pdb=" OG SER C 358 " pdb=" OG SER C 417 " model vdw 2.210 2.440 ... (remaining 484263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 24 through 193 or (resid 194 and (name N or name CA or nam \ e C or name O or name CB )) or resid 195 through 261 or (resid 262 through 270 a \ nd (name N or name CA or name C or name O or name CB )) or resid 271 through 273 \ or (resid 274 through 275 and (name N or name CA or name C or name O or name CB \ )) or resid 276 through 322 or (resid 323 through 324 and (name N or name CA or \ name C or name O or name CB )) or resid 325 through 521 or (resid 522 through 5 \ 24 and (name N or name CA or name C or name O or name CB )) or resid 525 through \ 615 or (resid 616 and (name N or name CA 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 354 or (resid 355 and (name N o \ r name CA or name C or name O or name CB )) or resid 356 through 421 or (resid 4 \ 22 and (name N or name CA or name C or name O or name CB )) or resid 423 through \ 521 or (resid 522 through 524 and (name N or name CA or name C or name O or nam \ e CB )) or resid 525 through 531 or (resid 532 and (name N or name CA or name C \ or name O or name CB )) or resid 533 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 t \ hrough 595 and (name N or name CA or name C or name O or name CB )) or resid 596 \ through 616)) selection = (chain 'E' and (resid 24 through 193 or (resid 194 and (name N or name CA or nam \ e C or name O or name CB )) or resid 195 through 261 or (resid 262 through 270 a \ nd (name N or name CA or name C or name O or name CB )) or resid 271 through 273 \ or (resid 274 through 275 and (name N or name CA or name C or name O or name CB \ )) or resid 276 through 284 or (resid 285 and (name N or name CA or name C or n \ ame O or name CB )) or resid 286 through 322 or (resid 323 through 324 and (name \ N or name CA or name C or name O or name CB )) or resid 325 through 354 or (res \ id 355 and (name N or name CA or name C or name O or name CB )) or resid 356 thr \ ough 421 or (resid 422 and (name N or name CA or name C or name O or name CB )) \ or resid 423 through 531 or (resid 532 and (name N or name CA or name C or name \ O or name CB )) or resid 533 through 589 or (resid 590 through 591 and (name N o \ r name CA or name C or name O or name CB )) or resid 592 or (resid 593 through 5 \ 95 and (name N or name CA or name C or name O or name CB )) or resid 596 through \ 615 or (resid 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 250 or (resid 251 and (name N or name CA or nam \ e C or name O or name CB )) or resid 252 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 250 or (resid 251 and (name N o \ r name CA or name C or name O or name CB )) or resid 252 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)) selection = (chain 'F' and ((resid 14 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB )) or resid 107 through 194 or (resid 195 and (name N \ or name CA or name C or name O or name CB )) or resid 196 through 204 or (resid \ 205 and (name N or name CA or name C or name O or name CB )) or resid 206 throug \ h 481 or (resid 482 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 113 or (resid 114 through 117 and (name N or nam \ e CA or name C or name O or name CB )) or resid 118 through 170 or (resid 171 an \ d (name N or name CA or name C or name O or name CB )) or resid 172 through 176 \ or (resid 177 and (name N or name 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 na \ me O or name CB )) or (resid 186 through 215 and (name N or name CA or name C or \ name O or name CB )) or resid 216 through 218 or (resid 219 through 223 and (na \ me 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 149 or (resid 150 through 151 and (name N or nam \ e CA or name C or name O or name CB )) or resid 152 through 158 or (resid 159 an \ d (name N or name CA or name C or name O or name CB )) or resid 160 through 169 \ or (resid 170 through 171 and (name N or name CA or name C or name O or name CB \ )) or resid 172 through 179 or (resid 180 through 185 and (name N or name CA or \ name C or name O or name CB )) or (resid 186 through 215 and (name N or name CA \ or name C or name O or name CB )) or resid 216 through 228)) selection = (chain 'K' and (resid 9 through 99 or (resid 100 through 108 and (name N or name \ CA or name C or name O or name CB )) or resid 109 or (resid 110 through 117 and \ (name N or name CA or name C or name O or name CB )) or resid 118 through 149 o \ r (resid 150 through 151 and (name N or name CA or name C or name O or name CB ) \ ) or resid 152 through 158 or (resid 159 and (name N or name CA or name C or nam \ e O or name CB )) or resid 160 through 169 or (resid 170 through 171 and (name N \ or name CA or name C or name O or name CB )) or resid 172 through 176 or (resid \ 177 and (name N or name CA or name C or name O or name CB )) or resid 178 throu \ gh 195 or (resid 196 through 215 and (name N or name CA or name C or name O or n \ ame CB )) or resid 216 through 217 or (resid 218 through 223 and (name N or name \ CA or name C or name O or name CB )) or resid 224 through 225 or (resid 226 thr \ ough 228 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = (chain 'H' and resid 2 through 112) selection = chain 'J' selection = chain 'L' } ncs_group { reference = (chain 'g' and (resid 3 through 80 or (resid 81 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 159)) selection = (chain 'h' and (resid 3 through 80 or (resid 81 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 159)) selection = (chain 'i' and (resid 3 through 80 or (resid 81 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 159)) selection = (chain 'j' and (resid 3 through 80 or (resid 81 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 159)) selection = (chain 'k' and (resid 3 through 80 or (resid 81 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 159)) selection = (chain 'l' and (resid 3 through 80 or (resid 81 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 159)) selection = (chain 'm' and (resid 3 through 80 or (resid 81 through 83 and (name N or name C \ A or name C or name O or name CB )) or resid 84 through 128 or (resid 129 and (n \ ame N or name CA or name C or name O or name CB )) or resid 130 through 159)) selection = (chain 'n' and (resid 3 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 159)) } 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 7.710 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 115.910 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.230 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:2.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 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 : 0.003 0.080 58786 Z= 0.223 Angle : 0.622 10.730 80171 Z= 0.331 Chirality : 0.043 0.270 9573 Planarity : 0.004 0.106 10454 Dihedral : 12.899 153.495 19767 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 0.12 % Allowed : 0.27 % Favored : 99.61 % 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: 1.40 (0.10), residues: 8152 helix: 1.99 (0.07), residues: 4729 sheet: -0.98 (0.20), residues: 618 loop : -0.40 (0.12), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 567 HIS 0.006 0.001 HIS a 729 PHE 0.044 0.002 PHE h 12 TYR 0.043 0.002 TYR l 85 ARG 0.011 0.001 ARG F 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1625 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1619 time to evaluate : 4.932 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 378 GLN cc_start: 0.8526 (mt0) cc_final: 0.8139 (mt0) REVERT: A 442 ASP cc_start: 0.8609 (t0) cc_final: 0.8322 (t0) REVERT: C 251 THR cc_start: 0.8753 (p) cc_final: 0.8323 (p) REVERT: C 295 MET cc_start: 0.8565 (ppp) cc_final: 0.7885 (ppp) REVERT: C 365 ARG cc_start: 0.8307 (ttt180) cc_final: 0.8066 (ttt180) REVERT: C 497 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8492 (tm-30) REVERT: C 608 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8198 (tm-30) REVERT: D 69 GLU cc_start: 0.5803 (tp30) cc_final: 0.4813 (tp30) REVERT: D 73 ASP cc_start: 0.8391 (p0) cc_final: 0.8099 (p0) REVERT: D 361 ASP cc_start: 0.8331 (t70) cc_final: 0.8120 (t0) REVERT: D 434 GLU cc_start: 0.8331 (tp30) cc_final: 0.8115 (tp30) REVERT: E 283 CYS cc_start: 0.9009 (t) cc_final: 0.8757 (t) REVERT: E 483 ASP cc_start: 0.8257 (m-30) cc_final: 0.7949 (m-30) REVERT: E 493 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7844 (mt-10) REVERT: E 496 GLU cc_start: 0.8272 (tp30) cc_final: 0.7907 (tp30) REVERT: E 511 ASP cc_start: 0.8390 (m-30) cc_final: 0.8002 (m-30) REVERT: F 13 LYS cc_start: 0.4312 (pptt) cc_final: 0.3627 (pttp) REVERT: F 277 ILE cc_start: 0.9189 (mm) cc_final: 0.8988 (mt) REVERT: F 429 ASP cc_start: 0.8491 (m-30) cc_final: 0.8198 (m-30) REVERT: G 155 ASP cc_start: 0.8701 (t70) cc_final: 0.8208 (t0) REVERT: G 162 GLU cc_start: 0.7704 (pm20) cc_final: 0.7443 (pm20) REVERT: K 123 SER cc_start: 0.9324 (t) cc_final: 0.9097 (t) REVERT: M 182 GLU cc_start: 0.8746 (tp30) cc_final: 0.8337 (tp30) REVERT: a 14 MET cc_start: 0.6358 (ptm) cc_final: 0.6033 (ptm) REVERT: a 80 ASP cc_start: 0.7410 (p0) cc_final: 0.7162 (p0) REVERT: a 430 PHE cc_start: 0.7652 (t80) cc_final: 0.7214 (t80) REVERT: a 432 MET cc_start: 0.8608 (ttp) cc_final: 0.8402 (tmm) REVERT: a 465 ILE cc_start: 0.8630 (pt) cc_final: 0.8382 (pt) REVERT: a 474 TYR cc_start: 0.8264 (t80) cc_final: 0.7635 (t80) REVERT: a 741 LEU cc_start: 0.9445 (mm) cc_final: 0.9155 (mm) REVERT: a 827 MET cc_start: 0.5314 (mmm) cc_final: 0.5036 (mmt) REVERT: b 258 THR cc_start: 0.8960 (p) cc_final: 0.8580 (p) REVERT: c 140 TYR cc_start: 0.8099 (t80) cc_final: 0.7857 (t80) REVERT: d 87 SER cc_start: 0.8889 (t) cc_final: 0.8615 (t) REVERT: d 194 ASN cc_start: 0.8607 (t0) cc_final: 0.8140 (t0) REVERT: d 206 GLU cc_start: 0.8127 (mp0) cc_final: 0.7909 (mp0) REVERT: e 43 MET cc_start: 0.8340 (ttm) cc_final: 0.8037 (ttm) REVERT: e 47 MET cc_start: 0.8764 (ttt) cc_final: 0.8495 (ttt) REVERT: g 21 ILE cc_start: 0.9204 (tp) cc_final: 0.8966 (tp) REVERT: g 49 LEU cc_start: 0.8258 (mt) cc_final: 0.8050 (mt) REVERT: g 63 ILE cc_start: 0.9281 (mm) cc_final: 0.8989 (mm) REVERT: g 151 ASN cc_start: 0.8174 (t0) cc_final: 0.7972 (t0) REVERT: h 54 ILE cc_start: 0.8559 (tp) cc_final: 0.8346 (tp) REVERT: h 77 SER cc_start: 0.8096 (p) cc_final: 0.7882 (p) REVERT: i 4 LEU cc_start: 0.8883 (mm) cc_final: 0.8675 (mm) REVERT: i 52 LYS cc_start: 0.8767 (ptmm) cc_final: 0.8402 (ptmm) REVERT: i 144 LEU cc_start: 0.9472 (tt) cc_final: 0.8967 (tp) REVERT: i 148 LEU cc_start: 0.9506 (mm) cc_final: 0.9129 (mm) REVERT: j 22 ILE cc_start: 0.8624 (mt) cc_final: 0.8420 (mt) REVERT: k 11 PHE cc_start: 0.8578 (t80) cc_final: 0.8354 (t80) REVERT: l 49 LEU cc_start: 0.9229 (mt) cc_final: 0.9009 (mt) REVERT: l 151 ASN cc_start: 0.8523 (t0) cc_final: 0.8313 (t0) REVERT: m 25 SER cc_start: 0.9141 (t) cc_final: 0.8872 (t) REVERT: m 34 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8556 (mptt) REVERT: m 85 TYR cc_start: 0.8772 (t80) cc_final: 0.8567 (t80) REVERT: m 86 THR cc_start: 0.7817 (p) cc_final: 0.7128 (p) REVERT: m 90 GLN cc_start: 0.8087 (mt0) cc_final: 0.7877 (mt0) REVERT: m 124 ARG cc_start: 0.7951 (tpt170) cc_final: 0.7430 (ttm-80) REVERT: m 145 ILE cc_start: 0.9317 (tp) cc_final: 0.8795 (tp) REVERT: m 149 LEU cc_start: 0.8726 (mt) cc_final: 0.8461 (mt) REVERT: n 52 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8235 (ttpp) REVERT: n 89 ILE cc_start: 0.8897 (mm) cc_final: 0.8631 (mm) REVERT: n 137 GLU cc_start: 0.8627 (tp30) cc_final: 0.8381 (tp30) REVERT: o 31 CYS cc_start: 0.8571 (t) cc_final: 0.8203 (t) REVERT: o 76 VAL cc_start: 0.9144 (t) cc_final: 0.8431 (t) REVERT: o 130 GLN cc_start: 0.8953 (pp30) cc_final: 0.8589 (pp30) outliers start: 6 outliers final: 0 residues processed: 1622 average time/residue: 0.5273 time to fit residues: 1474.3771 Evaluate side-chains 1413 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1413 time to evaluate : 4.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 681 optimal weight: 8.9990 chunk 611 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 208 optimal weight: 4.9990 chunk 412 optimal weight: 50.0000 chunk 326 optimal weight: 9.9990 chunk 632 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 384 optimal weight: 0.7980 chunk 470 optimal weight: 30.0000 chunk 732 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN A 450 HIS ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN D 181 ASN D 331 GLN E 53 HIS E 320 ASN E 497 GLN F 135 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 533 ASN ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 90 GLN n 90 GLN ** o 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 58786 Z= 0.492 Angle : 0.698 11.175 80171 Z= 0.377 Chirality : 0.046 0.225 9573 Planarity : 0.006 0.070 10454 Dihedral : 5.027 134.556 8732 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.06 % Favored : 95.93 % Rotamer: Outliers : 3.73 % Allowed : 13.28 % Favored : 82.99 % 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: 0.83 (0.09), residues: 8152 helix: 1.44 (0.07), residues: 4727 sheet: -0.96 (0.20), residues: 642 loop : -0.52 (0.12), residues: 2783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 802 HIS 0.010 0.001 HIS C 170 PHE 0.034 0.002 PHE a 419 TYR 0.041 0.002 TYR h 142 ARG 0.007 0.001 ARG E 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1652 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1460 time to evaluate : 5.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 GLN cc_start: 0.8350 (mt0) cc_final: 0.7949 (mt0) REVERT: A 442 ASP cc_start: 0.8602 (t0) cc_final: 0.8182 (t70) REVERT: A 569 LYS cc_start: 0.8910 (tptp) cc_final: 0.8703 (tptp) REVERT: B 251 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8079 (mt-10) REVERT: B 337 MET cc_start: 0.7356 (mmm) cc_final: 0.7113 (mtm) REVERT: B 417 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8764 (mmmm) REVERT: C 296 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7673 (mm-30) REVERT: C 365 ARG cc_start: 0.8389 (ttt180) cc_final: 0.8129 (ttt180) REVERT: C 497 GLN cc_start: 0.8930 (tm-30) cc_final: 0.8559 (tm-30) REVERT: C 608 GLN cc_start: 0.8609 (tm-30) cc_final: 0.8330 (tm-30) REVERT: D 73 ASP cc_start: 0.8431 (p0) cc_final: 0.8044 (p0) REVERT: D 352 TYR cc_start: 0.6556 (m-80) cc_final: 0.6315 (m-80) REVERT: D 434 GLU cc_start: 0.8325 (tp30) cc_final: 0.7981 (tp30) REVERT: E 289 GLU cc_start: 0.7850 (mp0) cc_final: 0.7276 (mp0) REVERT: E 483 ASP cc_start: 0.8263 (m-30) cc_final: 0.7901 (m-30) REVERT: E 496 GLU cc_start: 0.8340 (tp30) cc_final: 0.7962 (tp30) REVERT: E 511 ASP cc_start: 0.8326 (m-30) cc_final: 0.7763 (m-30) REVERT: F 13 LYS cc_start: 0.4067 (pptt) cc_final: 0.3246 (pttp) REVERT: F 223 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8389 (mtt90) REVERT: F 363 GLN cc_start: 0.8500 (mp10) cc_final: 0.8289 (mp10) REVERT: F 376 LEU cc_start: 0.9235 (tp) cc_final: 0.9024 (tp) REVERT: G 155 ASP cc_start: 0.8769 (t70) cc_final: 0.8286 (t0) REVERT: I 158 ARG cc_start: 0.8961 (ttp80) cc_final: 0.8400 (ptm-80) REVERT: K 122 GLN cc_start: 0.8712 (tt0) cc_final: 0.8506 (tt0) REVERT: K 123 SER cc_start: 0.9335 (t) cc_final: 0.9046 (t) REVERT: M 182 GLU cc_start: 0.8820 (tp30) cc_final: 0.8367 (tp30) REVERT: a 80 ASP cc_start: 0.7582 (p0) cc_final: 0.7262 (p0) REVERT: a 432 MET cc_start: 0.8738 (ttp) cc_final: 0.8307 (tmm) REVERT: a 474 TYR cc_start: 0.8414 (t80) cc_final: 0.7455 (t80) REVERT: a 537 MET cc_start: 0.8408 (mmm) cc_final: 0.8028 (mmm) REVERT: a 745 GLN cc_start: 0.8903 (mp10) cc_final: 0.8600 (mp10) REVERT: a 768 PHE cc_start: 0.8887 (t80) cc_final: 0.8608 (t80) REVERT: b 258 THR cc_start: 0.9112 (p) cc_final: 0.8853 (p) REVERT: c 138 ASN cc_start: 0.8054 (m-40) cc_final: 0.7583 (m-40) REVERT: c 140 TYR cc_start: 0.8154 (t80) cc_final: 0.7792 (t80) REVERT: c 196 LEU cc_start: 0.8995 (tp) cc_final: 0.8724 (tp) REVERT: d 87 SER cc_start: 0.9139 (t) cc_final: 0.8908 (t) REVERT: d 190 GLU cc_start: 0.7618 (mp0) cc_final: 0.7036 (mp0) REVERT: d 194 ASN cc_start: 0.8788 (t0) cc_final: 0.8329 (t0) REVERT: d 206 GLU cc_start: 0.8010 (mp0) cc_final: 0.7729 (mp0) REVERT: d 217 ASP cc_start: 0.8291 (m-30) cc_final: 0.7830 (m-30) REVERT: e 43 MET cc_start: 0.8289 (ttm) cc_final: 0.7678 (ttm) REVERT: e 47 MET cc_start: 0.8787 (ttt) cc_final: 0.8331 (ttt) REVERT: e 50 ILE cc_start: 0.8755 (mt) cc_final: 0.8118 (tp) REVERT: f 66 PHE cc_start: 0.8705 (t80) cc_final: 0.8497 (t80) REVERT: g 21 ILE cc_start: 0.9392 (tp) cc_final: 0.9176 (tp) REVERT: g 43 CYS cc_start: 0.7259 (p) cc_final: 0.6915 (p) REVERT: g 151 ASN cc_start: 0.8205 (t0) cc_final: 0.7713 (t0) REVERT: h 78 LEU cc_start: 0.8531 (tt) cc_final: 0.8164 (tt) REVERT: h 142 TYR cc_start: 0.8632 (m-80) cc_final: 0.8364 (m-80) REVERT: i 84 LEU cc_start: 0.9388 (tp) cc_final: 0.9055 (tp) REVERT: j 22 ILE cc_start: 0.8767 (mt) cc_final: 0.8512 (mt) REVERT: j 88 PHE cc_start: 0.8263 (m-80) cc_final: 0.8015 (m-80) REVERT: j 153 ARG cc_start: 0.8908 (ttm170) cc_final: 0.8688 (ttm170) REVERT: k 11 PHE cc_start: 0.8933 (t80) cc_final: 0.8689 (t80) REVERT: k 25 SER cc_start: 0.9241 (m) cc_final: 0.8897 (m) REVERT: k 122 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7613 (tm-30) REVERT: k 156 GLN cc_start: 0.8756 (pp30) cc_final: 0.8493 (pp30) REVERT: l 52 LYS cc_start: 0.7822 (mmtt) cc_final: 0.6911 (mtmt) REVERT: l 89 ILE cc_start: 0.9111 (mt) cc_final: 0.8651 (tt) REVERT: l 91 LEU cc_start: 0.9285 (tt) cc_final: 0.9005 (tp) REVERT: l 142 TYR cc_start: 0.8862 (m-10) cc_final: 0.8628 (m-10) REVERT: l 151 ASN cc_start: 0.8775 (t0) cc_final: 0.8565 (t0) REVERT: m 30 TYR cc_start: 0.8797 (t80) cc_final: 0.8583 (t80) REVERT: m 34 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8601 (mptt) REVERT: m 86 THR cc_start: 0.8030 (p) cc_final: 0.7307 (p) REVERT: m 90 GLN cc_start: 0.8326 (mt0) cc_final: 0.8090 (mt0) REVERT: m 124 ARG cc_start: 0.8133 (tpt170) cc_final: 0.7564 (ttm-80) REVERT: m 129 MET cc_start: 0.8611 (tmm) cc_final: 0.8268 (ttm) REVERT: m 145 ILE cc_start: 0.9541 (tp) cc_final: 0.9218 (tp) REVERT: m 149 LEU cc_start: 0.9021 (mt) cc_final: 0.8761 (mt) REVERT: o 130 GLN cc_start: 0.9079 (pp30) cc_final: 0.8711 (pp30) outliers start: 192 outliers final: 150 residues processed: 1523 average time/residue: 0.5226 time to fit residues: 1367.8527 Evaluate side-chains 1518 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1368 time to evaluate : 4.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 74 GLU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 543 THR Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 302 ARG Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 172 ILE Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain a residue 425 ASP Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 556 LEU Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 800 LEU Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain b residue 229 VAL Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 66 LEU Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 81 ILE Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 116 ILE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 151 THR Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain d residue 263 GLU Chi-restraints excluded: chain e residue 10 VAL Chi-restraints excluded: chain e residue 12 ILE Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain g residue 17 CYS Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 78 LEU Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 11 PHE Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 65 ILE Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 96 SER Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 146 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain i residue 134 ILE Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 69 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 77 SER Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 150 LEU Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 130 ILE Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain l residue 24 THR Chi-restraints excluded: chain l residue 75 CYS Chi-restraints excluded: chain l residue 148 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 49 LEU Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain m residue 110 ILE Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 35 SER Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 120 SER Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain o residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 407 optimal weight: 10.0000 chunk 227 optimal weight: 4.9990 chunk 609 optimal weight: 0.6980 chunk 499 optimal weight: 2.9990 chunk 202 optimal weight: 5.9990 chunk 734 optimal weight: 1.9990 chunk 793 optimal weight: 0.9990 chunk 653 optimal weight: 0.5980 chunk 728 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 588 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 533 ASN ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 ASN ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 GLN ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 334 GLN f 29 HIS ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 121 GLN ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 53 ASN m 90 GLN n 90 GLN ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 58786 Z= 0.200 Angle : 0.565 10.410 80171 Z= 0.300 Chirality : 0.042 0.218 9573 Planarity : 0.005 0.057 10454 Dihedral : 4.738 131.414 8732 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 3.65 % Allowed : 16.97 % Favored : 79.38 % 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: 0.90 (0.09), residues: 8152 helix: 1.46 (0.08), residues: 4723 sheet: -1.06 (0.19), residues: 636 loop : -0.40 (0.12), residues: 2793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 594 HIS 0.007 0.001 HIS f 29 PHE 0.040 0.001 PHE a 419 TYR 0.034 0.001 TYR c 143 ARG 0.007 0.000 ARG G 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1682 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1494 time to evaluate : 4.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 GLN cc_start: 0.8390 (mt0) cc_final: 0.7941 (mt0) REVERT: A 442 ASP cc_start: 0.8633 (t0) cc_final: 0.8386 (t0) REVERT: A 569 LYS cc_start: 0.8920 (tptp) cc_final: 0.8717 (tptp) REVERT: B 114 ASP cc_start: 0.8825 (t0) cc_final: 0.8426 (t0) REVERT: B 215 MET cc_start: 0.8313 (mtt) cc_final: 0.8058 (mtm) REVERT: B 251 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 260 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8983 (mm) REVERT: B 417 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8678 (mmmm) REVERT: B 472 MET cc_start: 0.8467 (mtm) cc_final: 0.7916 (mtm) REVERT: C 173 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8775 (pp) REVERT: C 295 MET cc_start: 0.8219 (ppp) cc_final: 0.6333 (ppp) REVERT: C 296 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7225 (mm-30) REVERT: C 497 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8543 (tm-30) REVERT: C 498 VAL cc_start: 0.9134 (OUTLIER) cc_final: 0.8870 (p) REVERT: C 608 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8274 (tm-30) REVERT: D 73 ASP cc_start: 0.8300 (p0) cc_final: 0.7999 (p0) REVERT: D 434 GLU cc_start: 0.8297 (tp30) cc_final: 0.8042 (tp30) REVERT: E 289 GLU cc_start: 0.7962 (mp0) cc_final: 0.7334 (mp0) REVERT: E 335 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8821 (p) REVERT: E 483 ASP cc_start: 0.8252 (m-30) cc_final: 0.7875 (m-30) REVERT: E 496 GLU cc_start: 0.8296 (tp30) cc_final: 0.7943 (tp30) REVERT: E 511 ASP cc_start: 0.8318 (m-30) cc_final: 0.7887 (m-30) REVERT: F 13 LYS cc_start: 0.3741 (pptt) cc_final: 0.2847 (pttp) REVERT: F 220 GLU cc_start: 0.8238 (tp30) cc_final: 0.8003 (tp30) REVERT: G 155 ASP cc_start: 0.8713 (t70) cc_final: 0.8257 (t0) REVERT: K 122 GLN cc_start: 0.8641 (tt0) cc_final: 0.8283 (tt0) REVERT: K 123 SER cc_start: 0.9299 (t) cc_final: 0.8995 (t) REVERT: M 15 LEU cc_start: 0.7708 (tp) cc_final: 0.7459 (tt) REVERT: M 182 GLU cc_start: 0.8774 (tp30) cc_final: 0.8367 (tp30) REVERT: a 80 ASP cc_start: 0.7613 (p0) cc_final: 0.7237 (p0) REVERT: a 432 MET cc_start: 0.8691 (ttp) cc_final: 0.8289 (tmm) REVERT: a 474 TYR cc_start: 0.8251 (t80) cc_final: 0.7266 (t80) REVERT: a 533 ASN cc_start: 0.8418 (m-40) cc_final: 0.8203 (m110) REVERT: a 537 MET cc_start: 0.8404 (mmm) cc_final: 0.8187 (mmm) REVERT: a 611 MET cc_start: 0.7286 (mmm) cc_final: 0.6963 (mmm) REVERT: a 741 LEU cc_start: 0.9489 (mm) cc_final: 0.9205 (mm) REVERT: a 768 PHE cc_start: 0.8825 (t80) cc_final: 0.8561 (t80) REVERT: b 258 THR cc_start: 0.9077 (p) cc_final: 0.8832 (p) REVERT: c 138 ASN cc_start: 0.7890 (m-40) cc_final: 0.7352 (m-40) REVERT: c 140 TYR cc_start: 0.8006 (t80) cc_final: 0.7683 (t80) REVERT: c 184 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8454 (mt) REVERT: d 190 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7081 (mp0) REVERT: d 194 ASN cc_start: 0.8656 (t0) cc_final: 0.8301 (t0) REVERT: d 206 GLU cc_start: 0.7975 (mp0) cc_final: 0.7741 (mp0) REVERT: e 47 MET cc_start: 0.8863 (ttt) cc_final: 0.8445 (ttt) REVERT: g 21 ILE cc_start: 0.9379 (tp) cc_final: 0.9127 (tp) REVERT: g 43 CYS cc_start: 0.7058 (p) cc_final: 0.6408 (p) REVERT: g 151 ASN cc_start: 0.8028 (t0) cc_final: 0.7432 (t0) REVERT: h 125 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8849 (tp) REVERT: h 142 TYR cc_start: 0.8506 (m-80) cc_final: 0.7978 (m-80) REVERT: i 52 LYS cc_start: 0.8757 (ptmm) cc_final: 0.8490 (ptmm) REVERT: i 88 PHE cc_start: 0.8567 (m-10) cc_final: 0.8347 (m-80) REVERT: j 88 PHE cc_start: 0.8180 (m-80) cc_final: 0.7878 (m-80) REVERT: j 122 GLN cc_start: 0.8745 (pp30) cc_final: 0.8339 (pp30) REVERT: k 11 PHE cc_start: 0.8874 (t80) cc_final: 0.8605 (t80) REVERT: k 25 SER cc_start: 0.9081 (m) cc_final: 0.8857 (m) REVERT: k 122 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7386 (tm-30) REVERT: k 156 GLN cc_start: 0.8764 (pp30) cc_final: 0.8445 (pp30) REVERT: l 52 LYS cc_start: 0.7756 (mmtt) cc_final: 0.6738 (mmpt) REVERT: l 85 TYR cc_start: 0.8673 (t80) cc_final: 0.8246 (t80) REVERT: l 89 ILE cc_start: 0.8950 (mt) cc_final: 0.8635 (tt) REVERT: l 90 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: m 34 LYS cc_start: 0.8942 (mmtt) cc_final: 0.8560 (mptt) REVERT: m 86 THR cc_start: 0.7984 (p) cc_final: 0.7242 (p) REVERT: m 117 ARG cc_start: 0.8464 (mmt-90) cc_final: 0.8208 (mmt-90) REVERT: m 124 ARG cc_start: 0.7999 (tpt170) cc_final: 0.7442 (ttm-80) REVERT: m 145 ILE cc_start: 0.9470 (tp) cc_final: 0.9089 (tp) REVERT: m 149 LEU cc_start: 0.9002 (mt) cc_final: 0.8732 (mt) REVERT: n 85 TYR cc_start: 0.8411 (t80) cc_final: 0.7754 (t80) REVERT: n 133 LEU cc_start: 0.9309 (tp) cc_final: 0.8541 (tp) REVERT: o 130 GLN cc_start: 0.8961 (pp30) cc_final: 0.8496 (pp30) outliers start: 188 outliers final: 128 residues processed: 1560 average time/residue: 0.5163 time to fit residues: 1379.2957 Evaluate side-chains 1547 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1412 time to evaluate : 4.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 569 LYS Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 302 ARG Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain a residue 402 TYR Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 753 MET Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 66 LEU Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain c residue 188 GLU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain d residue 165 CYS Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain g residue 17 CYS Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 55 VAL Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 78 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 77 SER Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 100 SER Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 130 ILE Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 148 LEU Chi-restraints excluded: chain m residue 148 LEU Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 139 LEU Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain o residue 146 VAL Chi-restraints excluded: chain o residue 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 725 optimal weight: 4.9990 chunk 551 optimal weight: 0.0980 chunk 381 optimal weight: 40.0000 chunk 81 optimal weight: 5.9990 chunk 350 optimal weight: 1.9990 chunk 492 optimal weight: 9.9990 chunk 736 optimal weight: 6.9990 chunk 780 optimal weight: 3.9990 chunk 384 optimal weight: 2.9990 chunk 698 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 GLN ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 58786 Z= 0.266 Angle : 0.582 9.862 80171 Z= 0.308 Chirality : 0.043 0.251 9573 Planarity : 0.005 0.056 10454 Dihedral : 4.664 117.826 8732 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.67 % Favored : 96.32 % Rotamer: Outliers : 4.52 % Allowed : 18.52 % Favored : 76.96 % 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: 0.87 (0.10), residues: 8152 helix: 1.43 (0.08), residues: 4728 sheet: -1.04 (0.19), residues: 635 loop : -0.40 (0.12), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP a 594 HIS 0.007 0.001 HIS C 170 PHE 0.041 0.002 PHE a 419 TYR 0.019 0.001 TYR h 142 ARG 0.009 0.000 ARG I 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1685 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1452 time to evaluate : 5.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 GLN cc_start: 0.8376 (mt0) cc_final: 0.7888 (mt0) REVERT: A 442 ASP cc_start: 0.8625 (t0) cc_final: 0.8376 (t0) REVERT: B 114 ASP cc_start: 0.8859 (t0) cc_final: 0.8497 (t0) REVERT: B 215 MET cc_start: 0.8354 (mtm) cc_final: 0.8082 (mtm) REVERT: B 231 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7439 (mt-10) REVERT: B 251 GLU cc_start: 0.8243 (mt-10) cc_final: 0.8032 (mt-10) REVERT: B 260 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9005 (mm) REVERT: B 337 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.6811 (mmm) REVERT: B 417 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8709 (mmmm) REVERT: B 472 MET cc_start: 0.8401 (mtm) cc_final: 0.7924 (mtm) REVERT: C 90 LYS cc_start: 0.8844 (mptt) cc_final: 0.8603 (mmmt) REVERT: C 173 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8732 (pp) REVERT: C 295 MET cc_start: 0.8127 (ppp) cc_final: 0.5955 (ppp) REVERT: C 296 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7381 (mm-30) REVERT: C 330 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8401 (tt0) REVERT: C 365 ARG cc_start: 0.8292 (ttt180) cc_final: 0.8032 (ttt180) REVERT: C 497 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8537 (tm-30) REVERT: C 498 VAL cc_start: 0.9151 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 608 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8253 (tm-30) REVERT: D 69 GLU cc_start: 0.6007 (tp30) cc_final: 0.4801 (tp30) REVERT: D 73 ASP cc_start: 0.8375 (p0) cc_final: 0.8026 (p0) REVERT: D 434 GLU cc_start: 0.8285 (tp30) cc_final: 0.7987 (tp30) REVERT: E 335 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.8865 (p) REVERT: E 483 ASP cc_start: 0.8319 (m-30) cc_final: 0.7886 (m-30) REVERT: E 496 GLU cc_start: 0.8368 (tp30) cc_final: 0.8063 (tp30) REVERT: E 511 ASP cc_start: 0.8348 (m-30) cc_final: 0.7784 (m-30) REVERT: F 13 LYS cc_start: 0.3582 (pptt) cc_final: 0.2603 (pttp) REVERT: G 155 ASP cc_start: 0.8718 (t70) cc_final: 0.8267 (t0) REVERT: I 158 ARG cc_start: 0.8898 (ttp80) cc_final: 0.8294 (ptm-80) REVERT: K 122 GLN cc_start: 0.8622 (tt0) cc_final: 0.8290 (tt0) REVERT: K 123 SER cc_start: 0.9305 (t) cc_final: 0.8984 (t) REVERT: M 182 GLU cc_start: 0.8792 (tp30) cc_final: 0.8412 (tp30) REVERT: a 80 ASP cc_start: 0.7716 (p0) cc_final: 0.7357 (p0) REVERT: a 474 TYR cc_start: 0.7844 (t80) cc_final: 0.6798 (t80) REVERT: a 537 MET cc_start: 0.8279 (mmm) cc_final: 0.7761 (mmm) REVERT: a 611 MET cc_start: 0.7360 (mmm) cc_final: 0.6917 (mmp) REVERT: a 741 LEU cc_start: 0.9490 (mm) cc_final: 0.9257 (mm) REVERT: a 745 GLN cc_start: 0.8904 (mp10) cc_final: 0.8544 (mp10) REVERT: a 768 PHE cc_start: 0.8776 (t80) cc_final: 0.8550 (t80) REVERT: b 258 THR cc_start: 0.9063 (p) cc_final: 0.8817 (p) REVERT: c 138 ASN cc_start: 0.7807 (m-40) cc_final: 0.7311 (m-40) REVERT: c 184 ILE cc_start: 0.8820 (mt) cc_final: 0.8495 (mt) REVERT: c 196 LEU cc_start: 0.8943 (tp) cc_final: 0.8690 (tp) REVERT: d 190 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7039 (mp0) REVERT: d 194 ASN cc_start: 0.8740 (t0) cc_final: 0.8394 (t0) REVERT: e 47 MET cc_start: 0.8883 (ttt) cc_final: 0.8532 (ttt) REVERT: f 62 TYR cc_start: 0.7759 (m-80) cc_final: 0.7093 (t80) REVERT: g 21 ILE cc_start: 0.9398 (tp) cc_final: 0.9159 (tp) REVERT: g 43 CYS cc_start: 0.7001 (p) cc_final: 0.6358 (p) REVERT: g 78 LEU cc_start: 0.8929 (tp) cc_final: 0.8721 (tp) REVERT: g 151 ASN cc_start: 0.8073 (t0) cc_final: 0.7873 (t0) REVERT: h 88 PHE cc_start: 0.7262 (m-80) cc_final: 0.6600 (m-80) REVERT: h 125 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8750 (tp) REVERT: h 142 TYR cc_start: 0.8527 (m-80) cc_final: 0.8264 (m-80) REVERT: i 52 LYS cc_start: 0.8789 (ptmm) cc_final: 0.8496 (ptmm) REVERT: j 88 PHE cc_start: 0.8274 (m-80) cc_final: 0.7946 (m-80) REVERT: j 89 ILE cc_start: 0.9339 (mm) cc_final: 0.9104 (tp) REVERT: j 122 GLN cc_start: 0.8728 (pp30) cc_final: 0.8183 (pp30) REVERT: k 122 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7797 (tm-30) REVERT: k 156 GLN cc_start: 0.8776 (pp30) cc_final: 0.8395 (pp30) REVERT: l 52 LYS cc_start: 0.7885 (mmtt) cc_final: 0.6891 (mmpt) REVERT: l 85 TYR cc_start: 0.8610 (t80) cc_final: 0.8242 (t80) REVERT: l 89 ILE cc_start: 0.8952 (mt) cc_final: 0.8620 (tt) REVERT: l 90 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: l 142 TYR cc_start: 0.8814 (m-10) cc_final: 0.8562 (m-10) REVERT: m 34 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8591 (mptt) REVERT: m 86 THR cc_start: 0.7972 (p) cc_final: 0.7636 (p) REVERT: m 124 ARG cc_start: 0.7991 (tpt170) cc_final: 0.7401 (ttm-80) REVERT: m 129 MET cc_start: 0.8575 (tmm) cc_final: 0.8273 (ttm) REVERT: m 145 ILE cc_start: 0.9477 (tp) cc_final: 0.9099 (tp) REVERT: m 149 LEU cc_start: 0.8979 (mt) cc_final: 0.8704 (mt) REVERT: n 85 TYR cc_start: 0.8552 (t80) cc_final: 0.7834 (t80) REVERT: n 95 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9095 (tt) REVERT: n 142 TYR cc_start: 0.8660 (m-10) cc_final: 0.8357 (m-80) REVERT: o 130 GLN cc_start: 0.8937 (pp30) cc_final: 0.8502 (pp30) REVERT: o 152 MET cc_start: 0.8705 (tpp) cc_final: 0.8465 (tpp) outliers start: 233 outliers final: 177 residues processed: 1540 average time/residue: 0.5131 time to fit residues: 1358.3653 Evaluate side-chains 1594 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1409 time to evaluate : 4.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 493 GLU Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 569 LYS Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 302 ARG Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain a residue 425 ASP Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 753 MET Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 66 LEU Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 188 GLU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 150 GLU Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 54 CYS Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain g residue 17 CYS Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 145 ILE Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 73 LEU Chi-restraints excluded: chain h residue 96 SER Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 130 ILE Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 108 ILE Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 148 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain m residue 148 LEU Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 17 CYS Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 35 SER Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 62 ILE Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain n residue 139 LEU Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain o residue 146 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 649 optimal weight: 9.9990 chunk 442 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 580 optimal weight: 0.9980 chunk 321 optimal weight: 20.0000 chunk 665 optimal weight: 8.9990 chunk 539 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 398 optimal weight: 0.1980 chunk 700 optimal weight: 0.9980 chunk 196 optimal weight: 7.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 201 GLN ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 82 GLN ** l 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 GLN ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 58786 Z= 0.225 Angle : 0.569 10.204 80171 Z= 0.300 Chirality : 0.042 0.289 9573 Planarity : 0.004 0.053 10454 Dihedral : 4.580 107.886 8732 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 4.78 % Allowed : 19.88 % Favored : 75.34 % 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: 0.94 (0.10), residues: 8152 helix: 1.49 (0.08), residues: 4705 sheet: -1.09 (0.19), residues: 641 loop : -0.33 (0.12), residues: 2806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP a 594 HIS 0.006 0.001 HIS C 170 PHE 0.040 0.002 PHE a 419 TYR 0.046 0.001 TYR D 352 ARG 0.006 0.000 ARG l 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 1475 time to evaluate : 4.932 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 85 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8827 (t) REVERT: A 442 ASP cc_start: 0.8619 (t0) cc_final: 0.8380 (t0) REVERT: B 114 ASP cc_start: 0.8864 (t0) cc_final: 0.8657 (t0) REVERT: B 215 MET cc_start: 0.8310 (mtm) cc_final: 0.8015 (mtm) REVERT: B 240 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8034 (tt) REVERT: B 251 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7992 (mt-10) REVERT: B 260 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8993 (mm) REVERT: B 337 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6709 (mmm) REVERT: B 472 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7992 (mtm) REVERT: C 173 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8725 (pp) REVERT: C 295 MET cc_start: 0.8155 (ppp) cc_final: 0.6368 (ppp) REVERT: C 296 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7327 (mm-30) REVERT: C 330 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8285 (tt0) REVERT: C 497 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8570 (tm-30) REVERT: C 498 VAL cc_start: 0.9087 (OUTLIER) cc_final: 0.8687 (p) REVERT: C 500 GLN cc_start: 0.9007 (mm-40) cc_final: 0.8666 (mm-40) REVERT: C 608 GLN cc_start: 0.8572 (tm-30) cc_final: 0.8259 (tm-30) REVERT: D 69 GLU cc_start: 0.5935 (tp30) cc_final: 0.4616 (tp30) REVERT: D 73 ASP cc_start: 0.8289 (p0) cc_final: 0.7989 (p0) REVERT: D 434 GLU cc_start: 0.8268 (tp30) cc_final: 0.8005 (tp30) REVERT: E 335 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.8886 (p) REVERT: E 483 ASP cc_start: 0.8383 (m-30) cc_final: 0.7920 (m-30) REVERT: E 496 GLU cc_start: 0.8267 (tp30) cc_final: 0.7896 (tp30) REVERT: E 511 ASP cc_start: 0.8347 (m-30) cc_final: 0.7778 (m-30) REVERT: F 13 LYS cc_start: 0.3554 (pptt) cc_final: 0.2547 (pttp) REVERT: F 437 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7962 (tm-30) REVERT: G 155 ASP cc_start: 0.8746 (t70) cc_final: 0.8301 (t0) REVERT: I 157 MET cc_start: 0.8990 (mtm) cc_final: 0.8775 (mtt) REVERT: I 158 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8643 (ttp80) REVERT: K 113 ASN cc_start: 0.8146 (t0) cc_final: 0.7652 (p0) REVERT: K 122 GLN cc_start: 0.8566 (tt0) cc_final: 0.8277 (tt0) REVERT: K 123 SER cc_start: 0.9354 (t) cc_final: 0.9043 (t) REVERT: M 13 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: M 23 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8608 (pttp) REVERT: M 182 GLU cc_start: 0.8687 (tp30) cc_final: 0.8300 (tp30) REVERT: a 80 ASP cc_start: 0.7800 (p0) cc_final: 0.7443 (p0) REVERT: a 432 MET cc_start: 0.8539 (ttp) cc_final: 0.8301 (tmm) REVERT: a 449 MET cc_start: 0.7116 (ppp) cc_final: 0.6913 (pmm) REVERT: a 474 TYR cc_start: 0.7781 (t80) cc_final: 0.6616 (t80) REVERT: a 611 MET cc_start: 0.7370 (mmm) cc_final: 0.6911 (mmp) REVERT: a 642 LEU cc_start: 0.9290 (mm) cc_final: 0.9066 (mm) REVERT: a 741 LEU cc_start: 0.9483 (OUTLIER) cc_final: 0.9214 (mm) REVERT: a 768 PHE cc_start: 0.8778 (t80) cc_final: 0.8540 (t80) REVERT: b 258 THR cc_start: 0.9044 (p) cc_final: 0.8807 (p) REVERT: c 59 TRP cc_start: 0.9055 (m100) cc_final: 0.8799 (m100) REVERT: c 138 ASN cc_start: 0.7763 (m-40) cc_final: 0.7200 (m110) REVERT: c 184 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8472 (mt) REVERT: d 130 LEU cc_start: 0.9154 (tp) cc_final: 0.8776 (mp) REVERT: d 186 LYS cc_start: 0.8821 (ttpp) cc_final: 0.7970 (tttm) REVERT: d 190 GLU cc_start: 0.7379 (mt-10) cc_final: 0.7044 (mp0) REVERT: d 194 ASN cc_start: 0.8729 (t0) cc_final: 0.8372 (t0) REVERT: d 206 GLU cc_start: 0.8108 (mp0) cc_final: 0.7509 (pm20) REVERT: d 278 PHE cc_start: 0.7710 (t80) cc_final: 0.7456 (t80) REVERT: e 47 MET cc_start: 0.8778 (ttt) cc_final: 0.8385 (ttt) REVERT: f 62 TYR cc_start: 0.7745 (m-80) cc_final: 0.7122 (t80) REVERT: g 21 ILE cc_start: 0.9331 (tp) cc_final: 0.9021 (tp) REVERT: g 43 CYS cc_start: 0.7028 (p) cc_final: 0.6290 (p) REVERT: g 151 ASN cc_start: 0.7960 (t0) cc_final: 0.7726 (t0) REVERT: h 30 TYR cc_start: 0.8846 (t80) cc_final: 0.8644 (t80) REVERT: h 78 LEU cc_start: 0.8482 (tt) cc_final: 0.8200 (tt) REVERT: h 125 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8727 (tp) REVERT: h 142 TYR cc_start: 0.8399 (m-80) cc_final: 0.8144 (m-80) REVERT: i 52 LYS cc_start: 0.8787 (ptmm) cc_final: 0.8497 (ptmm) REVERT: j 88 PHE cc_start: 0.8367 (m-80) cc_final: 0.8038 (m-80) REVERT: j 89 ILE cc_start: 0.9279 (mm) cc_final: 0.9036 (tp) REVERT: j 122 GLN cc_start: 0.8724 (pp30) cc_final: 0.8183 (pp30) REVERT: k 122 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7670 (tm-30) REVERT: k 156 GLN cc_start: 0.8747 (pp30) cc_final: 0.8352 (pp30) REVERT: l 4 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8543 (mp) REVERT: l 52 LYS cc_start: 0.7849 (mmtt) cc_final: 0.6853 (mmpt) REVERT: l 86 THR cc_start: 0.8792 (p) cc_final: 0.7766 (p) REVERT: l 89 ILE cc_start: 0.8973 (mt) cc_final: 0.8516 (tt) REVERT: l 90 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8085 (pm20) REVERT: l 106 PHE cc_start: 0.8670 (t80) cc_final: 0.8433 (t80) REVERT: m 34 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8571 (mptt) REVERT: m 86 THR cc_start: 0.7902 (p) cc_final: 0.7577 (p) REVERT: m 124 ARG cc_start: 0.7974 (tpt170) cc_final: 0.7375 (ttm-80) REVERT: m 145 ILE cc_start: 0.9473 (tp) cc_final: 0.9145 (tp) REVERT: m 149 LEU cc_start: 0.8943 (mt) cc_final: 0.8665 (mt) REVERT: n 85 TYR cc_start: 0.8512 (t80) cc_final: 0.7777 (t80) REVERT: n 95 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9086 (tt) REVERT: n 142 TYR cc_start: 0.8654 (m-10) cc_final: 0.8347 (m-80) REVERT: o 130 GLN cc_start: 0.8877 (pp30) cc_final: 0.8466 (pp30) REVERT: o 152 MET cc_start: 0.8681 (tpp) cc_final: 0.8454 (tpp) outliers start: 246 outliers final: 178 residues processed: 1569 average time/residue: 0.5138 time to fit residues: 1385.1796 Evaluate side-chains 1605 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1412 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 353 ILE Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 569 LYS Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 375 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 741 LEU Chi-restraints excluded: chain a residue 753 MET Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain c residue 188 GLU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain d residue 150 GLU Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 44 MET Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain g residue 17 CYS Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 55 VAL Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 141 LEU Chi-restraints excluded: chain g residue 145 ILE Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 44 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain h residue 119 SER Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 119 SER Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 133 LEU Chi-restraints excluded: chain k residue 76 TYR Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 108 ILE Chi-restraints excluded: chain l residue 148 LEU Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain m residue 148 LEU Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 35 SER Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 59 MET Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain n residue 139 LEU Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 145 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 262 optimal weight: 6.9990 chunk 702 optimal weight: 0.0170 chunk 154 optimal weight: 2.9990 chunk 457 optimal weight: 0.0030 chunk 192 optimal weight: 4.9990 chunk 780 optimal weight: 0.9990 chunk 648 optimal weight: 10.0000 chunk 361 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 409 optimal weight: 40.0000 overall best weight: 0.9832 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 GLN n 151 ASN ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 58786 Z= 0.182 Angle : 0.560 10.064 80171 Z= 0.293 Chirality : 0.042 0.257 9573 Planarity : 0.004 0.060 10454 Dihedral : 4.450 89.137 8732 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.35 % Favored : 96.64 % Rotamer: Outliers : 4.68 % Allowed : 20.97 % Favored : 74.35 % 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: 1.01 (0.10), residues: 8152 helix: 1.56 (0.08), residues: 4677 sheet: -1.10 (0.19), residues: 636 loop : -0.30 (0.12), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 567 HIS 0.005 0.001 HIS C 170 PHE 0.040 0.001 PHE h 12 TYR 0.039 0.001 TYR l 85 ARG 0.008 0.000 ARG j 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 241 poor density : 1496 time to evaluate : 4.950 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 85 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8817 (t) REVERT: A 442 ASP cc_start: 0.8603 (t0) cc_final: 0.8222 (t0) REVERT: B 215 MET cc_start: 0.8233 (mtm) cc_final: 0.7946 (mtm) REVERT: B 231 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 240 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7979 (tt) REVERT: B 251 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7880 (mt-10) REVERT: B 260 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9033 (mm) REVERT: B 337 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6680 (mmm) REVERT: B 417 LYS cc_start: 0.8869 (mmmm) cc_final: 0.8603 (mmmm) REVERT: B 472 MET cc_start: 0.8505 (mtm) cc_final: 0.8077 (mtm) REVERT: C 173 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8703 (pp) REVERT: C 295 MET cc_start: 0.8053 (ppp) cc_final: 0.6067 (ppp) REVERT: C 296 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7271 (mm-30) REVERT: C 330 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8303 (tt0) REVERT: C 365 ARG cc_start: 0.8241 (ttt180) cc_final: 0.8023 (ttt180) REVERT: C 497 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8579 (tm-30) REVERT: C 498 VAL cc_start: 0.9140 (OUTLIER) cc_final: 0.8880 (p) REVERT: C 500 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8667 (mm-40) REVERT: C 608 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8212 (tm-30) REVERT: D 69 GLU cc_start: 0.5890 (tp30) cc_final: 0.4525 (tp30) REVERT: D 73 ASP cc_start: 0.8214 (p0) cc_final: 0.7923 (p0) REVERT: D 348 ASP cc_start: 0.8160 (m-30) cc_final: 0.7612 (m-30) REVERT: D 434 GLU cc_start: 0.8335 (tp30) cc_final: 0.8046 (tp30) REVERT: E 101 MET cc_start: 0.8290 (mmm) cc_final: 0.7833 (mmm) REVERT: E 289 GLU cc_start: 0.7927 (mp0) cc_final: 0.7289 (mp0) REVERT: E 292 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7741 (mt-10) REVERT: E 335 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8893 (p) REVERT: E 483 ASP cc_start: 0.8319 (m-30) cc_final: 0.7855 (m-30) REVERT: E 496 GLU cc_start: 0.8240 (tp30) cc_final: 0.7842 (tp30) REVERT: E 511 ASP cc_start: 0.8360 (m-30) cc_final: 0.7792 (m-30) REVERT: F 13 LYS cc_start: 0.3722 (pptt) cc_final: 0.2746 (pttp) REVERT: F 416 MET cc_start: 0.8269 (tpp) cc_final: 0.7952 (tpt) REVERT: G 155 ASP cc_start: 0.8712 (t70) cc_final: 0.8270 (t0) REVERT: I 158 ARG cc_start: 0.8843 (ttp80) cc_final: 0.8627 (ttp80) REVERT: K 113 ASN cc_start: 0.8149 (t0) cc_final: 0.7551 (p0) REVERT: K 122 GLN cc_start: 0.8563 (tt0) cc_final: 0.8300 (tt0) REVERT: K 123 SER cc_start: 0.9305 (t) cc_final: 0.8979 (t) REVERT: M 13 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.8098 (mmm) REVERT: M 23 LYS cc_start: 0.9003 (ttpp) cc_final: 0.8489 (pttt) REVERT: M 57 MET cc_start: 0.8673 (tmm) cc_final: 0.7922 (tmm) REVERT: M 182 GLU cc_start: 0.8708 (tp30) cc_final: 0.8313 (tp30) REVERT: a 80 ASP cc_start: 0.7812 (p0) cc_final: 0.7454 (p0) REVERT: a 432 MET cc_start: 0.8491 (ttp) cc_final: 0.8183 (tmm) REVERT: a 474 TYR cc_start: 0.7833 (t80) cc_final: 0.6741 (t80) REVERT: a 537 MET cc_start: 0.8211 (mmm) cc_final: 0.7982 (mmm) REVERT: a 611 MET cc_start: 0.7305 (mmm) cc_final: 0.6833 (mmp) REVERT: a 768 PHE cc_start: 0.8776 (t80) cc_final: 0.8539 (t80) REVERT: b 258 THR cc_start: 0.9023 (p) cc_final: 0.8792 (p) REVERT: c 138 ASN cc_start: 0.7620 (m-40) cc_final: 0.7102 (m110) REVERT: c 184 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8441 (mt) REVERT: d 87 SER cc_start: 0.9220 (t) cc_final: 0.8824 (t) REVERT: d 130 LEU cc_start: 0.9104 (tp) cc_final: 0.8815 (mp) REVERT: d 190 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7169 (mp0) REVERT: d 194 ASN cc_start: 0.8726 (t0) cc_final: 0.8304 (t0) REVERT: d 206 GLU cc_start: 0.8100 (mp0) cc_final: 0.7582 (pm20) REVERT: e 44 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6285 (tpt) REVERT: e 47 MET cc_start: 0.8811 (ttt) cc_final: 0.8417 (ttt) REVERT: g 21 ILE cc_start: 0.9299 (tp) cc_final: 0.8980 (tp) REVERT: g 43 CYS cc_start: 0.7004 (p) cc_final: 0.6204 (p) REVERT: g 59 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.7012 (mtt) REVERT: g 151 ASN cc_start: 0.7937 (t0) cc_final: 0.7271 (t0) REVERT: h 78 LEU cc_start: 0.8479 (tt) cc_final: 0.8015 (tt) REVERT: h 125 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8600 (tp) REVERT: j 88 PHE cc_start: 0.8449 (m-80) cc_final: 0.8107 (m-80) REVERT: j 122 GLN cc_start: 0.8714 (pp30) cc_final: 0.8451 (pp30) REVERT: k 11 PHE cc_start: 0.8668 (t80) cc_final: 0.8464 (t80) REVERT: k 30 TYR cc_start: 0.8908 (t80) cc_final: 0.8682 (t80) REVERT: k 122 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7679 (tm-30) REVERT: k 156 GLN cc_start: 0.8680 (pp30) cc_final: 0.8281 (pp30) REVERT: l 30 TYR cc_start: 0.8770 (t80) cc_final: 0.8469 (t80) REVERT: l 52 LYS cc_start: 0.7848 (mmtt) cc_final: 0.6840 (mmpt) REVERT: l 86 THR cc_start: 0.8729 (p) cc_final: 0.7933 (p) REVERT: l 88 PHE cc_start: 0.7866 (m-80) cc_final: 0.7479 (m-80) REVERT: l 90 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: l 142 TYR cc_start: 0.8814 (m-10) cc_final: 0.8508 (m-10) REVERT: m 34 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8628 (mptt) REVERT: m 86 THR cc_start: 0.7894 (p) cc_final: 0.7641 (p) REVERT: m 121 GLN cc_start: 0.8724 (mp10) cc_final: 0.8085 (mp10) REVERT: m 124 ARG cc_start: 0.7916 (tpt170) cc_final: 0.7353 (ttm-80) REVERT: m 149 LEU cc_start: 0.8944 (mt) cc_final: 0.8709 (mt) REVERT: n 50 LEU cc_start: 0.8764 (tt) cc_final: 0.8497 (tp) REVERT: n 59 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.8022 (mtp) REVERT: n 85 TYR cc_start: 0.8463 (t80) cc_final: 0.7778 (t80) REVERT: n 95 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.9046 (tt) REVERT: n 137 GLU cc_start: 0.8904 (tp30) cc_final: 0.8658 (tp30) REVERT: o 130 GLN cc_start: 0.8801 (pp30) cc_final: 0.8459 (pp30) outliers start: 241 outliers final: 175 residues processed: 1588 average time/residue: 0.5220 time to fit residues: 1432.0556 Evaluate side-chains 1628 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1438 time to evaluate : 4.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 476 ILE Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 569 LYS Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 239 SER Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 302 ARG Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 136 LYS Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 13 MET Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 190 SER Chi-restraints excluded: chain M residue 200 PHE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain a residue 370 VAL Chi-restraints excluded: chain a residue 478 LEU Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 753 MET Chi-restraints excluded: chain a residue 800 LEU Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain c residue 188 GLU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 150 GLU Chi-restraints excluded: chain d residue 165 CYS Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 44 MET Chi-restraints excluded: chain e residue 46 LEU Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain g residue 17 CYS Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 55 VAL Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 71 SER Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 145 ILE Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 44 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 4 LEU Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain i residue 25 SER Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 76 TYR Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 108 ILE Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 133 LEU Chi-restraints excluded: chain l residue 148 LEU Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain m residue 148 LEU Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 35 SER Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 59 MET Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 139 LEU Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 101 CYS Chi-restraints excluded: chain o residue 145 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 752 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 444 optimal weight: 30.0000 chunk 570 optimal weight: 20.0000 chunk 441 optimal weight: 6.9990 chunk 657 optimal weight: 0.8980 chunk 436 optimal weight: 9.9990 chunk 777 optimal weight: 0.6980 chunk 486 optimal weight: 0.9990 chunk 474 optimal weight: 40.0000 chunk 359 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 183 ASN ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 90 GLN ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 58786 Z= 0.259 Angle : 0.589 10.361 80171 Z= 0.308 Chirality : 0.043 0.295 9573 Planarity : 0.004 0.052 10454 Dihedral : 4.457 76.646 8732 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.58 % Favored : 96.41 % Rotamer: Outliers : 4.99 % Allowed : 21.84 % Favored : 73.17 % 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: 1.00 (0.10), residues: 8152 helix: 1.55 (0.08), residues: 4679 sheet: -1.03 (0.19), residues: 631 loop : -0.32 (0.12), residues: 2842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP a 594 HIS 0.007 0.001 HIS C 170 PHE 0.067 0.002 PHE h 88 TYR 0.049 0.001 TYR D 352 ARG 0.008 0.000 ARG M 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1693 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1436 time to evaluate : 4.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8612 (t0) cc_final: 0.8365 (t0) REVERT: B 215 MET cc_start: 0.8303 (mtm) cc_final: 0.7992 (mtm) REVERT: B 240 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8068 (tt) REVERT: B 251 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 260 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9014 (mm) REVERT: B 337 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6704 (mmm) REVERT: B 472 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8009 (mtm) REVERT: C 173 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8721 (pp) REVERT: C 295 MET cc_start: 0.8033 (ppp) cc_final: 0.6115 (ppp) REVERT: C 296 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7272 (mm-30) REVERT: C 330 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8329 (tt0) REVERT: C 497 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8554 (tm-30) REVERT: C 498 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8889 (p) REVERT: C 608 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8201 (tm-30) REVERT: D 69 GLU cc_start: 0.5893 (tp30) cc_final: 0.4463 (tp30) REVERT: D 73 ASP cc_start: 0.8328 (p0) cc_final: 0.8003 (p0) REVERT: D 348 ASP cc_start: 0.8176 (m-30) cc_final: 0.7613 (m-30) REVERT: D 434 GLU cc_start: 0.8301 (tp30) cc_final: 0.8002 (tp30) REVERT: E 335 THR cc_start: 0.9258 (OUTLIER) cc_final: 0.8887 (p) REVERT: E 483 ASP cc_start: 0.8369 (m-30) cc_final: 0.7912 (m-30) REVERT: E 496 GLU cc_start: 0.8267 (tp30) cc_final: 0.7888 (tp30) REVERT: F 13 LYS cc_start: 0.3833 (pptt) cc_final: 0.2838 (pttp) REVERT: F 219 LEU cc_start: 0.9154 (tt) cc_final: 0.8865 (tt) REVERT: F 223 ARG cc_start: 0.8867 (mtt90) cc_final: 0.8589 (mtt90) REVERT: F 416 MET cc_start: 0.8281 (tpp) cc_final: 0.7962 (tpt) REVERT: G 155 ASP cc_start: 0.8758 (t70) cc_final: 0.8324 (t0) REVERT: I 158 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8564 (ttp80) REVERT: K 113 ASN cc_start: 0.8195 (t0) cc_final: 0.7595 (p0) REVERT: K 122 GLN cc_start: 0.8555 (tt0) cc_final: 0.8354 (tt0) REVERT: K 123 SER cc_start: 0.9351 (t) cc_final: 0.9027 (t) REVERT: M 23 LYS cc_start: 0.8989 (ttpp) cc_final: 0.8608 (pttt) REVERT: M 57 MET cc_start: 0.8694 (tmm) cc_final: 0.8083 (tmm) REVERT: M 182 GLU cc_start: 0.8788 (tp30) cc_final: 0.8409 (tp30) REVERT: a 80 ASP cc_start: 0.7852 (p0) cc_final: 0.7484 (p0) REVERT: a 426 MET cc_start: 0.7968 (tpp) cc_final: 0.7681 (mmt) REVERT: a 432 MET cc_start: 0.8499 (ttp) cc_final: 0.8158 (tmm) REVERT: a 449 MET cc_start: 0.7325 (ppp) cc_final: 0.6800 (pmm) REVERT: a 537 MET cc_start: 0.8225 (mmm) cc_final: 0.8002 (mmm) REVERT: a 642 LEU cc_start: 0.9363 (mm) cc_final: 0.9105 (mm) REVERT: a 745 GLN cc_start: 0.9000 (mp10) cc_final: 0.8612 (mp10) REVERT: a 768 PHE cc_start: 0.8783 (t80) cc_final: 0.8550 (t80) REVERT: b 258 THR cc_start: 0.9037 (p) cc_final: 0.8801 (p) REVERT: c 138 ASN cc_start: 0.7743 (m-40) cc_final: 0.7193 (m110) REVERT: c 184 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8501 (mt) REVERT: c 194 LEU cc_start: 0.9275 (mm) cc_final: 0.9003 (mt) REVERT: d 130 LEU cc_start: 0.9137 (tp) cc_final: 0.8831 (mp) REVERT: d 190 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7160 (mt-10) REVERT: d 194 ASN cc_start: 0.8754 (t0) cc_final: 0.8385 (t0) REVERT: d 206 GLU cc_start: 0.8110 (mp0) cc_final: 0.7575 (pm20) REVERT: d 297 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8191 (ttm-80) REVERT: e 44 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6336 (tpt) REVERT: f 62 TYR cc_start: 0.7856 (m-80) cc_final: 0.7390 (t80) REVERT: g 21 ILE cc_start: 0.9304 (tp) cc_final: 0.8984 (tp) REVERT: g 43 CYS cc_start: 0.6920 (p) cc_final: 0.6214 (p) REVERT: g 59 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7165 (mtt) REVERT: h 125 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8643 (tp) REVERT: h 142 TYR cc_start: 0.8360 (m-80) cc_final: 0.7796 (m-80) REVERT: j 52 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8799 (tppt) REVERT: j 88 PHE cc_start: 0.8435 (m-80) cc_final: 0.8205 (m-80) REVERT: j 122 GLN cc_start: 0.8700 (pp30) cc_final: 0.8459 (pp30) REVERT: k 11 PHE cc_start: 0.8637 (t80) cc_final: 0.8427 (t80) REVERT: k 30 TYR cc_start: 0.8920 (t80) cc_final: 0.8716 (t80) REVERT: k 122 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7712 (tm-30) REVERT: l 4 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8833 (mt) REVERT: l 52 LYS cc_start: 0.8046 (mmtt) cc_final: 0.6979 (mmpt) REVERT: l 88 PHE cc_start: 0.8040 (m-80) cc_final: 0.7685 (m-80) REVERT: l 90 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: l 142 TYR cc_start: 0.8860 (m-10) cc_final: 0.8548 (m-10) REVERT: m 34 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8635 (mptt) REVERT: m 65 ILE cc_start: 0.9476 (mm) cc_final: 0.9035 (mm) REVERT: m 86 THR cc_start: 0.7966 (p) cc_final: 0.7702 (p) REVERT: m 121 GLN cc_start: 0.8763 (mp10) cc_final: 0.8120 (mp10) REVERT: m 124 ARG cc_start: 0.7961 (tpt170) cc_final: 0.7396 (ttm-80) REVERT: m 149 LEU cc_start: 0.8948 (mt) cc_final: 0.8677 (mt) REVERT: n 85 TYR cc_start: 0.8625 (t80) cc_final: 0.7832 (t80) REVERT: o 130 GLN cc_start: 0.8848 (pp30) cc_final: 0.8470 (pp30) outliers start: 257 outliers final: 211 residues processed: 1532 average time/residue: 0.5278 time to fit residues: 1399.8646 Evaluate side-chains 1639 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1414 time to evaluate : 4.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 498 VAL Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 569 LYS Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 302 ARG Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 200 PHE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain a residue 370 VAL Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 556 LEU Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 753 MET Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 71 SER Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 80 PHE Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 119 ILE Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain c residue 188 GLU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 150 GLU Chi-restraints excluded: chain d residue 165 CYS Chi-restraints excluded: chain d residue 189 LEU Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain d residue 263 GLU Chi-restraints excluded: chain d residue 297 ARG Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 39 LEU Chi-restraints excluded: chain e residue 44 MET Chi-restraints excluded: chain e residue 46 LEU Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain g residue 17 CYS Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 55 VAL Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 111 VAL Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 44 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 4 LEU Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 73 LEU Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 4 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain k residue 76 TYR Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 108 ILE Chi-restraints excluded: chain l residue 133 LEU Chi-restraints excluded: chain l residue 148 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain m residue 148 LEU Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 35 SER Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 59 MET Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 139 LEU Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 101 CYS Chi-restraints excluded: chain o residue 145 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 481 optimal weight: 20.0000 chunk 310 optimal weight: 5.9990 chunk 464 optimal weight: 30.0000 chunk 234 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 494 optimal weight: 0.9990 chunk 529 optimal weight: 4.9990 chunk 384 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 611 optimal weight: 0.0870 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** M 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 90 GLN m 82 GLN m 90 GLN n 90 GLN o 98 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 58786 Z= 0.327 Angle : 0.628 10.761 80171 Z= 0.329 Chirality : 0.044 0.334 9573 Planarity : 0.005 0.067 10454 Dihedral : 4.550 74.037 8732 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.93 % Favored : 96.06 % Rotamer: Outliers : 5.24 % Allowed : 22.15 % Favored : 72.61 % 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: 0.90 (0.10), residues: 8152 helix: 1.46 (0.08), residues: 4696 sheet: -1.00 (0.19), residues: 638 loop : -0.38 (0.12), residues: 2818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP a 594 HIS 0.007 0.001 HIS C 170 PHE 0.044 0.002 PHE a 419 TYR 0.045 0.002 TYR l 85 ARG 0.007 0.001 ARG E 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1680 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 1410 time to evaluate : 4.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8602 (t0) cc_final: 0.8330 (t0) REVERT: B 215 MET cc_start: 0.8413 (mtm) cc_final: 0.8124 (mtm) REVERT: B 251 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8054 (mt-10) REVERT: B 260 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9037 (mm) REVERT: B 337 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6676 (mmm) REVERT: B 472 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8059 (mtm) REVERT: C 173 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8714 (pp) REVERT: C 330 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8343 (tt0) REVERT: C 365 ARG cc_start: 0.8326 (ttt180) cc_final: 0.8075 (ttt180) REVERT: C 497 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8576 (tm-30) REVERT: C 498 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8921 (p) REVERT: C 500 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8694 (mm-40) REVERT: C 608 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8254 (tm-30) REVERT: D 69 GLU cc_start: 0.5977 (tp30) cc_final: 0.4651 (tp30) REVERT: D 73 ASP cc_start: 0.8337 (p0) cc_final: 0.7949 (p0) REVERT: D 361 ASP cc_start: 0.8292 (t70) cc_final: 0.8079 (t0) REVERT: D 434 GLU cc_start: 0.8315 (tp30) cc_final: 0.8001 (tp30) REVERT: E 101 MET cc_start: 0.8312 (mmm) cc_final: 0.8039 (mmm) REVERT: E 335 THR cc_start: 0.9285 (OUTLIER) cc_final: 0.8861 (p) REVERT: E 483 ASP cc_start: 0.8381 (m-30) cc_final: 0.7968 (m-30) REVERT: E 496 GLU cc_start: 0.8328 (tp30) cc_final: 0.8084 (tp30) REVERT: E 511 ASP cc_start: 0.8327 (m-30) cc_final: 0.7741 (m-30) REVERT: F 13 LYS cc_start: 0.3772 (pptt) cc_final: 0.2760 (pttp) REVERT: G 155 ASP cc_start: 0.8762 (t70) cc_final: 0.8325 (t0) REVERT: I 158 ARG cc_start: 0.8792 (ttp80) cc_final: 0.8533 (ttp80) REVERT: K 113 ASN cc_start: 0.8255 (t0) cc_final: 0.7597 (p0) REVERT: K 122 GLN cc_start: 0.8619 (tt0) cc_final: 0.8091 (tt0) REVERT: K 123 SER cc_start: 0.9355 (t) cc_final: 0.9022 (t) REVERT: M 23 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8641 (pttt) REVERT: M 57 MET cc_start: 0.8751 (tmm) cc_final: 0.8081 (tmm) REVERT: M 169 ARG cc_start: 0.8530 (tmm-80) cc_final: 0.8244 (ttp80) REVERT: M 182 GLU cc_start: 0.8822 (tp30) cc_final: 0.8487 (tp30) REVERT: a 80 ASP cc_start: 0.7896 (p0) cc_final: 0.7514 (p0) REVERT: a 449 MET cc_start: 0.7408 (ppp) cc_final: 0.7018 (pmm) REVERT: a 537 MET cc_start: 0.8178 (mmm) cc_final: 0.7973 (mmm) REVERT: a 611 MET cc_start: 0.7482 (mmm) cc_final: 0.7125 (mmm) REVERT: a 642 LEU cc_start: 0.9354 (mm) cc_final: 0.9107 (mm) REVERT: a 768 PHE cc_start: 0.8776 (t80) cc_final: 0.8549 (t80) REVERT: a 802 TRP cc_start: 0.8390 (m100) cc_final: 0.8028 (m100) REVERT: c 138 ASN cc_start: 0.7851 (m-40) cc_final: 0.7289 (m110) REVERT: c 184 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8573 (mt) REVERT: c 194 LEU cc_start: 0.9272 (mm) cc_final: 0.8981 (mt) REVERT: d 130 LEU cc_start: 0.9201 (tp) cc_final: 0.8916 (mp) REVERT: d 132 TRP cc_start: 0.8671 (t-100) cc_final: 0.8406 (t-100) REVERT: d 190 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7170 (mt-10) REVERT: d 194 ASN cc_start: 0.8812 (t0) cc_final: 0.8446 (t0) REVERT: d 206 GLU cc_start: 0.8147 (mp0) cc_final: 0.7613 (pm20) REVERT: d 278 PHE cc_start: 0.7891 (t80) cc_final: 0.7639 (t80) REVERT: d 297 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8194 (ttm-80) REVERT: e 44 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6292 (tpt) REVERT: f 62 TYR cc_start: 0.7885 (m-80) cc_final: 0.7387 (t80) REVERT: g 21 ILE cc_start: 0.9315 (tp) cc_final: 0.8999 (tp) REVERT: g 43 CYS cc_start: 0.6951 (p) cc_final: 0.6166 (p) REVERT: g 59 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7268 (mtt) REVERT: h 125 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8699 (tp) REVERT: h 142 TYR cc_start: 0.8452 (m-80) cc_final: 0.7835 (m-80) REVERT: i 3 GLU cc_start: 0.8784 (pp20) cc_final: 0.8420 (pp20) REVERT: j 52 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8799 (tppt) REVERT: j 84 LEU cc_start: 0.9067 (tp) cc_final: 0.8779 (tp) REVERT: j 88 PHE cc_start: 0.8444 (m-80) cc_final: 0.8094 (m-80) REVERT: j 122 GLN cc_start: 0.8705 (pp30) cc_final: 0.8466 (pp30) REVERT: k 30 TYR cc_start: 0.8913 (t80) cc_final: 0.8704 (t80) REVERT: k 122 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7984 (tm-30) REVERT: k 156 GLN cc_start: 0.8774 (pm20) cc_final: 0.8301 (pm20) REVERT: l 4 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8828 (mt) REVERT: l 52 LYS cc_start: 0.8025 (mmtt) cc_final: 0.6924 (mmpt) REVERT: l 88 PHE cc_start: 0.8260 (m-80) cc_final: 0.8015 (m-80) REVERT: l 90 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7934 (pm20) REVERT: m 34 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8645 (mptt) REVERT: m 121 GLN cc_start: 0.8795 (mp10) cc_final: 0.8153 (mp10) REVERT: m 124 ARG cc_start: 0.7990 (tpt170) cc_final: 0.7410 (ttm-80) REVERT: n 85 TYR cc_start: 0.8688 (t80) cc_final: 0.7864 (t80) REVERT: o 130 GLN cc_start: 0.8895 (pp30) cc_final: 0.8480 (pp30) outliers start: 270 outliers final: 220 residues processed: 1517 average time/residue: 0.5215 time to fit residues: 1362.4498 Evaluate side-chains 1620 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1387 time to evaluate : 4.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 TYR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 485 MET Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 607 MET Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 139 ILE Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 569 LYS Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 302 ARG Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 352 TYR Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 154 ASP Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 177 ASP Chi-restraints excluded: chain I residue 148 LEU Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 172 ILE Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 32 LEU Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 200 PHE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 370 VAL Chi-restraints excluded: chain a residue 383 THR Chi-restraints excluded: chain a residue 404 GLU Chi-restraints excluded: chain a residue 518 LEU Chi-restraints excluded: chain a residue 556 LEU Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 753 MET Chi-restraints excluded: chain b residue 215 LEU Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 233 LEU Chi-restraints excluded: chain c residue 30 ILE Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 71 SER Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain c residue 188 GLU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 150 GLU Chi-restraints excluded: chain d residue 189 LEU Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain d residue 263 GLU Chi-restraints excluded: chain d residue 297 ARG Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 20 LEU Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 44 MET Chi-restraints excluded: chain f residue 44 ASP Chi-restraints excluded: chain g residue 17 CYS Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 55 VAL Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 130 ILE Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain g residue 150 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 44 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 96 SER Chi-restraints excluded: chain h residue 100 SER Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 4 LEU Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain i residue 37 VAL Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 96 SER Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 108 ILE Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 127 VAL Chi-restraints excluded: chain j residue 130 ILE Chi-restraints excluded: chain j residue 150 LEU Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 73 LEU Chi-restraints excluded: chain k residue 76 TYR Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 89 ILE Chi-restraints excluded: chain k residue 100 SER Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain k residue 141 LEU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 25 SER Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 62 ILE Chi-restraints excluded: chain l residue 71 SER Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 108 ILE Chi-restraints excluded: chain l residue 133 LEU Chi-restraints excluded: chain l residue 148 LEU Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 35 SER Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 59 MET Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 77 SER Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 139 LEU Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 30 SER Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain o residue 101 CYS Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain o residue 160 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 707 optimal weight: 0.0980 chunk 745 optimal weight: 0.7980 chunk 679 optimal weight: 6.9990 chunk 724 optimal weight: 0.5980 chunk 744 optimal weight: 7.9990 chunk 436 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 chunk 569 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 654 optimal weight: 1.9990 chunk 685 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN M 211 GLN a 18 GLN ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 303 GLN ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN n 151 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 58786 Z= 0.175 Angle : 0.598 11.791 80171 Z= 0.307 Chirality : 0.043 0.309 9573 Planarity : 0.004 0.052 10454 Dihedral : 4.400 75.290 8732 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.96 % Allowed : 23.90 % Favored : 72.14 % 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: 0.98 (0.10), residues: 8152 helix: 1.51 (0.08), residues: 4700 sheet: -0.96 (0.20), residues: 614 loop : -0.33 (0.12), residues: 2838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 594 HIS 0.004 0.001 HIS C 170 PHE 0.042 0.001 PHE a 419 TYR 0.037 0.001 TYR l 85 ARG 0.010 0.000 ARG F 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1691 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1487 time to evaluate : 4.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 ASP cc_start: 0.8594 (t0) cc_final: 0.8347 (t0) REVERT: B 251 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7747 (mt-10) REVERT: B 260 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9015 (mm) REVERT: B 337 MET cc_start: 0.7198 (OUTLIER) cc_final: 0.6629 (mmm) REVERT: B 417 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8624 (mmmm) REVERT: B 472 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8098 (mtm) REVERT: C 173 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8709 (pp) REVERT: C 295 MET cc_start: 0.8105 (ppp) cc_final: 0.6203 (ppp) REVERT: C 296 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7242 (mm-30) REVERT: C 330 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8295 (tt0) REVERT: C 497 GLN cc_start: 0.8923 (tm-30) cc_final: 0.8575 (tm-30) REVERT: C 498 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8681 (p) REVERT: C 500 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8734 (mm-40) REVERT: C 504 LYS cc_start: 0.8944 (mttp) cc_final: 0.8662 (mttp) REVERT: C 608 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8204 (tm-30) REVERT: D 69 GLU cc_start: 0.5697 (tp30) cc_final: 0.4381 (tp30) REVERT: D 73 ASP cc_start: 0.8217 (p0) cc_final: 0.7940 (p0) REVERT: D 286 ASP cc_start: 0.8328 (m-30) cc_final: 0.8063 (m-30) REVERT: D 348 ASP cc_start: 0.8124 (m-30) cc_final: 0.7618 (m-30) REVERT: D 434 GLU cc_start: 0.8374 (tp30) cc_final: 0.8080 (tp30) REVERT: E 101 MET cc_start: 0.8171 (mmm) cc_final: 0.7746 (mmm) REVERT: E 335 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8893 (p) REVERT: E 392 TYR cc_start: 0.9325 (m-80) cc_final: 0.9108 (m-80) REVERT: E 483 ASP cc_start: 0.8355 (m-30) cc_final: 0.7922 (m-30) REVERT: E 485 MET cc_start: 0.8734 (mtp) cc_final: 0.8489 (mtm) REVERT: E 496 GLU cc_start: 0.8407 (tp30) cc_final: 0.8157 (tp30) REVERT: F 13 LYS cc_start: 0.3737 (pptt) cc_final: 0.2549 (pttp) REVERT: F 219 LEU cc_start: 0.9040 (tt) cc_final: 0.8616 (tt) REVERT: F 223 ARG cc_start: 0.8721 (mtt-85) cc_final: 0.8416 (mtt90) REVERT: F 404 TYR cc_start: 0.8746 (m-80) cc_final: 0.8385 (m-80) REVERT: F 416 MET cc_start: 0.8261 (tpp) cc_final: 0.7941 (tpt) REVERT: G 155 ASP cc_start: 0.8684 (t70) cc_final: 0.8154 (t0) REVERT: I 158 ARG cc_start: 0.8783 (ttp80) cc_final: 0.7920 (ptt-90) REVERT: K 113 ASN cc_start: 0.8161 (t0) cc_final: 0.7571 (p0) REVERT: K 122 GLN cc_start: 0.8430 (tt0) cc_final: 0.8152 (tt0) REVERT: K 123 SER cc_start: 0.9303 (t) cc_final: 0.8981 (t) REVERT: M 23 LYS cc_start: 0.8988 (ttpp) cc_final: 0.8508 (pttt) REVERT: M 57 MET cc_start: 0.8776 (tmm) cc_final: 0.7999 (tmm) REVERT: M 182 GLU cc_start: 0.8801 (tp30) cc_final: 0.8454 (tp30) REVERT: a 80 ASP cc_start: 0.7886 (p0) cc_final: 0.7516 (p0) REVERT: a 426 MET cc_start: 0.8100 (tpp) cc_final: 0.7775 (mmt) REVERT: a 432 MET cc_start: 0.8701 (ttp) cc_final: 0.8224 (tmm) REVERT: a 449 MET cc_start: 0.7324 (ppp) cc_final: 0.6844 (pmm) REVERT: a 611 MET cc_start: 0.7338 (mmm) cc_final: 0.7037 (mmm) REVERT: c 138 ASN cc_start: 0.7664 (m-40) cc_final: 0.7205 (m110) REVERT: c 184 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8432 (mt) REVERT: c 194 LEU cc_start: 0.9242 (mm) cc_final: 0.8955 (mt) REVERT: d 130 LEU cc_start: 0.9075 (tp) cc_final: 0.8795 (mp) REVERT: d 190 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7124 (mp0) REVERT: d 194 ASN cc_start: 0.8698 (t0) cc_final: 0.8279 (t0) REVERT: d 206 GLU cc_start: 0.8045 (mp0) cc_final: 0.7516 (pm20) REVERT: d 209 GLN cc_start: 0.8332 (mt0) cc_final: 0.7504 (mp10) REVERT: d 293 MET cc_start: 0.8513 (mmm) cc_final: 0.8085 (mmm) REVERT: e 44 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6253 (tpt) REVERT: f 62 TYR cc_start: 0.7721 (m-80) cc_final: 0.7156 (t80) REVERT: g 21 ILE cc_start: 0.9274 (tp) cc_final: 0.8958 (tp) REVERT: g 43 CYS cc_start: 0.6598 (p) cc_final: 0.6059 (p) REVERT: h 78 LEU cc_start: 0.8445 (tt) cc_final: 0.7886 (tt) REVERT: h 125 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8599 (tp) REVERT: h 142 TYR cc_start: 0.8358 (m-80) cc_final: 0.7878 (m-80) REVERT: i 3 GLU cc_start: 0.8706 (pp20) cc_final: 0.8399 (pp20) REVERT: i 85 TYR cc_start: 0.8884 (t80) cc_final: 0.8493 (t80) REVERT: j 84 LEU cc_start: 0.8846 (tp) cc_final: 0.8634 (tp) REVERT: j 88 PHE cc_start: 0.8286 (m-80) cc_final: 0.8019 (m-80) REVERT: j 117 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7601 (mmt90) REVERT: k 122 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7515 (tm-30) REVERT: k 156 GLN cc_start: 0.8832 (pm20) cc_final: 0.8499 (pm20) REVERT: l 4 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8712 (mt) REVERT: l 34 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8065 (mtpp) REVERT: l 52 LYS cc_start: 0.7613 (mmtt) cc_final: 0.6496 (mmpt) REVERT: l 90 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: l 142 TYR cc_start: 0.8841 (m-10) cc_final: 0.8517 (m-10) REVERT: m 34 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8598 (mptt) REVERT: m 52 LYS cc_start: 0.7750 (tptt) cc_final: 0.7493 (tppt) REVERT: m 121 GLN cc_start: 0.8679 (mp10) cc_final: 0.8052 (mp10) REVERT: m 124 ARG cc_start: 0.7864 (tpt170) cc_final: 0.7320 (ttm-80) REVERT: m 149 LEU cc_start: 0.8902 (mt) cc_final: 0.8665 (mt) REVERT: n 85 TYR cc_start: 0.8571 (t80) cc_final: 0.7797 (t80) REVERT: o 130 GLN cc_start: 0.8765 (pp30) cc_final: 0.8424 (pp30) outliers start: 204 outliers final: 162 residues processed: 1565 average time/residue: 0.5138 time to fit residues: 1386.7546 Evaluate side-chains 1592 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 1419 time to evaluate : 4.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 472 MET Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain E residue 501 LEU Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 569 LYS Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 315 ILE Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 145 ASP Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain I residue 166 ARG Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 200 PHE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain M residue 208 GLU Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 370 VAL Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 753 MET Chi-restraints excluded: chain a residue 800 LEU Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain c residue 188 GLU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 150 GLU Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 44 MET Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 55 VAL Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 145 ILE Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain h residue 125 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 149 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 4 LEU Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 127 VAL Chi-restraints excluded: chain j residue 150 LEU Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 55 VAL Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 42 THR Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 108 ILE Chi-restraints excluded: chain l residue 133 LEU Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 35 SER Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 64 VAL Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain o residue 101 CYS Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain o residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 722 optimal weight: 0.8980 chunk 475 optimal weight: 6.9990 chunk 766 optimal weight: 0.0980 chunk 467 optimal weight: 20.0000 chunk 363 optimal weight: 0.9990 chunk 532 optimal weight: 5.9990 chunk 803 optimal weight: 0.9980 chunk 739 optimal weight: 1.9990 chunk 640 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 494 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 533 ASN ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 151 ASN k 90 GLN ** l 53 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: 0.7811 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 58786 Z= 0.185 Angle : 0.609 12.320 80171 Z= 0.313 Chirality : 0.043 0.319 9573 Planarity : 0.004 0.049 10454 Dihedral : 4.348 75.496 8732 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.59 % Allowed : 25.02 % Favored : 71.38 % 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: 1.03 (0.10), residues: 8152 helix: 1.53 (0.08), residues: 4711 sheet: -0.89 (0.20), residues: 614 loop : -0.29 (0.12), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP a 594 HIS 0.005 0.001 HIS C 170 PHE 0.050 0.002 PHE o 93 TYR 0.043 0.001 TYR d 249 ARG 0.009 0.000 ARG C 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16304 Ramachandran restraints generated. 8152 Oldfield, 0 Emsley, 8152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1480 time to evaluate : 4.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ASP cc_start: 0.8692 (m-30) cc_final: 0.8232 (m-30) REVERT: A 240 LEU cc_start: 0.8786 (pp) cc_final: 0.8517 (pp) REVERT: A 442 ASP cc_start: 0.8600 (t0) cc_final: 0.8332 (t0) REVERT: A 472 ASP cc_start: 0.9105 (m-30) cc_final: 0.8887 (m-30) REVERT: B 231 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7332 (mt-10) REVERT: B 251 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7870 (mt-10) REVERT: B 260 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9023 (mm) REVERT: B 337 MET cc_start: 0.7185 (OUTLIER) cc_final: 0.6629 (mmm) REVERT: B 472 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8141 (mtm) REVERT: C 90 LYS cc_start: 0.8786 (mptt) cc_final: 0.8579 (mmmt) REVERT: C 173 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8797 (pp) REVERT: C 295 MET cc_start: 0.8040 (ppp) cc_final: 0.6036 (ppp) REVERT: C 296 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7274 (mm-30) REVERT: C 330 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8390 (tt0) REVERT: C 365 ARG cc_start: 0.8264 (ttt180) cc_final: 0.8012 (ttt180) REVERT: C 497 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8573 (tm-30) REVERT: C 498 VAL cc_start: 0.9050 (OUTLIER) cc_final: 0.8653 (p) REVERT: C 500 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8704 (mm-40) REVERT: C 608 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8172 (tm-30) REVERT: D 69 GLU cc_start: 0.5658 (tp30) cc_final: 0.4306 (tp30) REVERT: D 73 ASP cc_start: 0.8210 (p0) cc_final: 0.7936 (p0) REVERT: D 150 MET cc_start: 0.8697 (ttt) cc_final: 0.8063 (ttt) REVERT: D 348 ASP cc_start: 0.8137 (m-30) cc_final: 0.7693 (m-30) REVERT: D 434 GLU cc_start: 0.8375 (tp30) cc_final: 0.8084 (tp30) REVERT: E 101 MET cc_start: 0.8200 (mmm) cc_final: 0.7688 (mmm) REVERT: E 335 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8901 (p) REVERT: E 392 TYR cc_start: 0.9329 (m-80) cc_final: 0.9119 (m-80) REVERT: E 483 ASP cc_start: 0.8340 (m-30) cc_final: 0.7881 (m-30) REVERT: E 496 GLU cc_start: 0.8404 (tp30) cc_final: 0.8162 (tp30) REVERT: F 13 LYS cc_start: 0.3630 (pptt) cc_final: 0.2515 (pttp) REVERT: F 219 LEU cc_start: 0.9079 (tt) cc_final: 0.8673 (tt) REVERT: F 223 ARG cc_start: 0.8735 (mtt-85) cc_final: 0.8451 (mtt90) REVERT: F 416 MET cc_start: 0.8257 (tpp) cc_final: 0.7944 (tpt) REVERT: G 155 ASP cc_start: 0.8435 (t70) cc_final: 0.8125 (t0) REVERT: I 158 ARG cc_start: 0.8737 (ttp80) cc_final: 0.7934 (ptt-90) REVERT: K 113 ASN cc_start: 0.8150 (t0) cc_final: 0.7568 (p0) REVERT: K 123 SER cc_start: 0.9301 (t) cc_final: 0.8996 (t) REVERT: M 23 LYS cc_start: 0.9003 (ttpp) cc_final: 0.8540 (pttm) REVERT: M 57 MET cc_start: 0.8788 (tmm) cc_final: 0.7989 (tmm) REVERT: M 182 GLU cc_start: 0.8805 (tp30) cc_final: 0.8457 (tp30) REVERT: a 80 ASP cc_start: 0.7915 (p0) cc_final: 0.7539 (p0) REVERT: a 426 MET cc_start: 0.8051 (tpp) cc_final: 0.7779 (mmt) REVERT: a 449 MET cc_start: 0.7333 (ppp) cc_final: 0.6798 (pmm) REVERT: a 566 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7220 (tt) REVERT: a 611 MET cc_start: 0.7239 (mmm) cc_final: 0.6949 (mmm) REVERT: a 745 GLN cc_start: 0.8894 (mp10) cc_final: 0.8287 (mp10) REVERT: c 138 ASN cc_start: 0.7663 (m-40) cc_final: 0.7265 (m-40) REVERT: c 184 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8469 (mt) REVERT: d 130 LEU cc_start: 0.9065 (tp) cc_final: 0.8769 (mp) REVERT: d 190 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7054 (mp0) REVERT: d 194 ASN cc_start: 0.8726 (t0) cc_final: 0.8324 (t0) REVERT: d 206 GLU cc_start: 0.8012 (mp0) cc_final: 0.7461 (pm20) REVERT: d 293 MET cc_start: 0.8545 (mmm) cc_final: 0.8125 (mmm) REVERT: e 44 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6268 (tpt) REVERT: f 62 TYR cc_start: 0.7666 (m-80) cc_final: 0.7107 (t80) REVERT: g 21 ILE cc_start: 0.9278 (tp) cc_final: 0.8946 (tp) REVERT: g 43 CYS cc_start: 0.6812 (p) cc_final: 0.6151 (p) REVERT: g 153 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7514 (ttm-80) REVERT: h 142 TYR cc_start: 0.8256 (m-80) cc_final: 0.7863 (m-80) REVERT: i 3 GLU cc_start: 0.8689 (pp20) cc_final: 0.8395 (pp20) REVERT: i 110 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8632 (mt) REVERT: j 84 LEU cc_start: 0.8818 (tp) cc_final: 0.8445 (tp) REVERT: j 85 TYR cc_start: 0.8009 (t80) cc_final: 0.7770 (t80) REVERT: j 88 PHE cc_start: 0.8212 (m-80) cc_final: 0.7898 (m-80) REVERT: k 122 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7486 (tm-30) REVERT: k 156 GLN cc_start: 0.8797 (pm20) cc_final: 0.8402 (pm20) REVERT: l 4 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8569 (mt) REVERT: l 34 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8007 (mtpp) REVERT: l 50 LEU cc_start: 0.8908 (tp) cc_final: 0.8519 (pp) REVERT: l 52 LYS cc_start: 0.7476 (mmtt) cc_final: 0.6349 (mmpt) REVERT: l 90 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: l 113 ASP cc_start: 0.8428 (t0) cc_final: 0.8082 (t0) REVERT: l 117 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7991 (mmt90) REVERT: l 142 TYR cc_start: 0.8820 (m-10) cc_final: 0.8439 (m-10) REVERT: m 34 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8592 (mptt) REVERT: m 52 LYS cc_start: 0.7759 (tptt) cc_final: 0.7519 (tppt) REVERT: m 124 ARG cc_start: 0.7758 (tpt170) cc_final: 0.7280 (ttm-80) REVERT: m 149 LEU cc_start: 0.8928 (mt) cc_final: 0.8689 (mt) REVERT: n 122 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7613 (tm-30) REVERT: o 130 GLN cc_start: 0.8771 (pp30) cc_final: 0.8396 (pp30) outliers start: 185 outliers final: 154 residues processed: 1552 average time/residue: 0.5114 time to fit residues: 1365.8300 Evaluate side-chains 1592 residues out of total 6931 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 1426 time to evaluate : 4.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 472 MET Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 427 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain D residue 34 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 188 CYS Chi-restraints excluded: chain D residue 215 MET Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 230 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 382 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 333 ILE Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain E residue 561 VAL Chi-restraints excluded: chain E residue 569 LYS Chi-restraints excluded: chain E residue 573 SER Chi-restraints excluded: chain F residue 78 GLN Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 419 VAL Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain G residue 140 LYS Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain I residue 176 ASN Chi-restraints excluded: chain K residue 174 ILE Chi-restraints excluded: chain K residue 202 THR Chi-restraints excluded: chain K residue 228 THR Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 61 MET Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain M residue 200 PHE Chi-restraints excluded: chain M residue 203 LEU Chi-restraints excluded: chain a residue 344 ASP Chi-restraints excluded: chain a residue 349 LEU Chi-restraints excluded: chain a residue 370 VAL Chi-restraints excluded: chain a residue 475 THR Chi-restraints excluded: chain a residue 566 ILE Chi-restraints excluded: chain a residue 730 THR Chi-restraints excluded: chain a residue 753 MET Chi-restraints excluded: chain a residue 800 LEU Chi-restraints excluded: chain b residue 232 LEU Chi-restraints excluded: chain b residue 238 ILE Chi-restraints excluded: chain c residue 67 CYS Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 98 THR Chi-restraints excluded: chain c residue 150 ILE Chi-restraints excluded: chain c residue 159 CYS Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain c residue 188 GLU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 203 LEU Chi-restraints excluded: chain c residue 205 MET Chi-restraints excluded: chain d residue 9 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 83 ILE Chi-restraints excluded: chain d residue 150 GLU Chi-restraints excluded: chain d residue 165 CYS Chi-restraints excluded: chain d residue 320 VAL Chi-restraints excluded: chain e residue 35 SER Chi-restraints excluded: chain e residue 44 MET Chi-restraints excluded: chain g residue 25 SER Chi-restraints excluded: chain g residue 39 ILE Chi-restraints excluded: chain g residue 45 LEU Chi-restraints excluded: chain g residue 55 VAL Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain g residue 89 ILE Chi-restraints excluded: chain g residue 95 LEU Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 138 VAL Chi-restraints excluded: chain g residue 148 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 4 LEU Chi-restraints excluded: chain h residue 37 VAL Chi-restraints excluded: chain h residue 44 VAL Chi-restraints excluded: chain h residue 55 VAL Chi-restraints excluded: chain h residue 59 MET Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 108 ILE Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain h residue 149 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 17 CYS Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 51 PHE Chi-restraints excluded: chain i residue 63 ILE Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 70 VAL Chi-restraints excluded: chain i residue 110 ILE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 15 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 73 LEU Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 110 ILE Chi-restraints excluded: chain j residue 119 SER Chi-restraints excluded: chain j residue 130 ILE Chi-restraints excluded: chain j residue 150 LEU Chi-restraints excluded: chain k residue 42 THR Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain k residue 86 THR Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 139 LEU Chi-restraints excluded: chain k residue 146 VAL Chi-restraints excluded: chain k residue 149 LEU Chi-restraints excluded: chain k residue 150 LEU Chi-restraints excluded: chain l residue 4 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain l residue 90 GLN Chi-restraints excluded: chain l residue 108 ILE Chi-restraints excluded: chain l residue 133 LEU Chi-restraints excluded: chain m residue 25 SER Chi-restraints excluded: chain m residue 70 VAL Chi-restraints excluded: chain m residue 100 SER Chi-restraints excluded: chain m residue 150 LEU Chi-restraints excluded: chain n residue 24 THR Chi-restraints excluded: chain n residue 25 SER Chi-restraints excluded: chain n residue 35 SER Chi-restraints excluded: chain n residue 44 VAL Chi-restraints excluded: chain n residue 63 ILE Chi-restraints excluded: chain n residue 95 LEU Chi-restraints excluded: chain n residue 97 VAL Chi-restraints excluded: chain n residue 100 SER Chi-restraints excluded: chain n residue 134 ILE Chi-restraints excluded: chain n residue 155 THR Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 91 THR Chi-restraints excluded: chain o residue 101 CYS Chi-restraints excluded: chain o residue 145 GLU Chi-restraints excluded: chain o residue 160 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 807 random chunks: chunk 392 optimal weight: 10.0000 chunk 508 optimal weight: 0.9980 chunk 681 optimal weight: 0.9990 chunk 196 optimal weight: 0.9980 chunk 590 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 641 optimal weight: 0.5980 chunk 268 optimal weight: 5.9990 chunk 658 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 320 ASN ** F 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 82 GLN n 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.117432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098128 restraints weight = 128302.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.100263 restraints weight = 62057.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.101599 restraints weight = 38428.294| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 58786 Z= 0.188 Angle : 0.609 12.584 80171 Z= 0.313 Chirality : 0.043 0.319 9573 Planarity : 0.005 0.099 10454 Dihedral : 4.327 75.501 8732 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.77 % Allowed : 24.83 % Favored : 71.40 % 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: 8152 helix: 1.56 (0.08), residues: 4709 sheet: -0.80 (0.20), residues: 620 loop : -0.27 (0.12), residues: 2823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP a 594 HIS 0.005 0.001 HIS C 170 PHE 0.041 0.001 PHE o 93 TYR 0.036 0.001 TYR d 249 ARG 0.008 0.000 ARG F 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18136.27 seconds wall clock time: 315 minutes 53.91 seconds (18953.91 seconds total)