Starting phenix.real_space_refine on Thu Mar 21 07:42:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g34_29688/03_2024/8g34_29688.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g34_29688/03_2024/8g34_29688.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g34_29688/03_2024/8g34_29688.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g34_29688/03_2024/8g34_29688.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g34_29688/03_2024/8g34_29688.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g34_29688/03_2024/8g34_29688.pdb" } resolution = 3.2 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= 0.006 sd= 0.056 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 4556 5.49 5 S 146 5.16 5 C 72703 2.51 5 N 26894 2.21 5 O 39957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 35": "OE1" <-> "OE2" Residue "1 PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 50": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D ASP 176": "OD1" <-> "OD2" Residue "E GLU 2": "OE1" <-> "OE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ASP 122": "OD1" <-> "OD2" Residue "F ASP 162": "OD1" <-> "OD2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "K TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 106": "OD1" <-> "OD2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "P PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 109": "OD1" <-> "OD2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "6 ASP 3": "OD1" <-> "OD2" Residue "6 GLU 25": "OE1" <-> "OE2" Residue "6 GLU 29": "OE1" <-> "OE2" Residue "6 GLU 40": "OE1" <-> "OE2" Residue "6 GLU 60": "OE1" <-> "OE2" Residue "6 GLU 119": "OE1" <-> "OE2" Residue "6 ASP 233": "OD1" <-> "OD2" Residue "6 PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 293": "OE1" <-> "OE2" Residue "6 ASP 320": "OD1" <-> "OD2" Residue "6 GLU 333": "OE1" <-> "OE2" Residue "6 GLU 390": "OE1" <-> "OE2" Residue "6 GLU 418": "OE1" <-> "OE2" Residue "x PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 160": "OE1" <-> "OE2" Residue "x TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 14": "OD1" <-> "OD2" Residue "f GLU 89": "OE1" <-> "OE2" Residue "h GLU 35": "OE1" <-> "OE2" Residue "h GLU 41": "OE1" <-> "OE2" Residue "i ASP 63": "OD1" <-> "OD2" Residue "l GLU 71": "OE1" <-> "OE2" Residue "r GLU 72": "OE1" <-> "OE2" Residue "u GLU 179": "OE1" <-> "OE2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w ASP 81": "OD1" <-> "OD2" Residue "w PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 174": "OE1" <-> "OE2" Residue "w PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 191": "OD1" <-> "OD2" Residue "c GLU 171": "OE1" <-> "OE2" Residue "c GLU 196": "OE1" <-> "OE2" Residue "e GLU 69": "OE1" <-> "OE2" Residue "g GLU 51": "OE1" <-> "OE2" Residue "g TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 89": "OD1" <-> "OD2" Residue "j PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 5": "OE1" <-> "OE2" Residue "n GLU 25": "OE1" <-> "OE2" Residue "o PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ASP 14": "OD1" <-> "OD2" Residue "p GLU 48": "OE1" <-> "OE2" Residue "q GLU 19": "OE1" <-> "OE2" Residue "s PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144256 Number of models: 1 Model: "" Number of chains: 52 Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2504 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 11, 'rna3p': 105} Chain: "B" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 269, 'rna2p_pyr': 153, 'rna3p_pur': 1405, 'rna3p_pyr': 1076} Link IDs: {'rna2p': 422, 'rna3p': 2480} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "6" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3403 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 410} Chain: "x" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "f" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "i" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "l" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "m" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "r" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "u" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 468 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "w" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "d" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1106 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "e" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "j" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "k" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "n" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "o" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "q" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "s" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "t" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "v" Number of atoms: 33010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33010 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 125, 'rna2p_pyr': 98, 'rna3p_pur': 748, 'rna3p_pyr': 568} Link IDs: {'rna2p': 222, 'rna3p': 1316} Time building chain proxies: 56.53, per 1000 atoms: 0.39 Number of scatterers: 144256 At special positions: 0 Unit cell: (242.05, 252.35, 271.92, 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 146 16.00 P 4556 15.00 O 39957 8.00 N 26894 7.00 C 72703 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: 60.42 Conformation dependent library (CDL) restraints added in 7.1 seconds 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10882 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 71 sheets defined 35.3% alpha, 17.3% beta 1468 base pairs and 2449 stacking pairs defined. Time for finding SS restraints: 52.83 Creating SS restraints... Processing helix chain '0' and resid 8 through 16 Processing helix chain '0' and resid 17 through 19 No H-bonds generated for 'chain '0' and resid 17 through 19' Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.000A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 36 through 44 Processing helix chain '3' and resid 53 through 61 Processing helix chain '4' and resid 30 through 34 removed outlier: 3.771A pdb=" N LYS 4 34 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.944A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.975A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'D' and resid 61 through 70 Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.534A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 21 removed outlier: 4.010A pdb=" N ARG E 21 " --> pdb=" O THR E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 46 through 56 Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 162 through 168 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.890A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 98 through 109 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'K' and resid 110 through 118 removed outlier: 4.008A pdb=" N ILE K 114 " --> pdb=" O LYS K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 79 through 85 removed outlier: 3.958A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 98 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'M' and resid 43 through 58 Processing helix chain 'M' and resid 109 through 124 removed outlier: 3.875A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 removed outlier: 4.291A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 82 Processing helix chain 'O' and resid 3 through 22 removed outlier: 4.803A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 3.914A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 85 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 96 through 102 removed outlier: 3.723A pdb=" N ARG P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 20 Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 3.543A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.585A pdb=" N ALA Q 98 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.974A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.802A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 18 through 28 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'V' and resid 13 through 23 Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.753A pdb=" N GLU V 59 " --> pdb=" O GLU V 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 62 Processing helix chain 'X' and resid 62 through 74 removed outlier: 3.575A pdb=" N VAL X 66 " --> pdb=" O GLY X 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 22 Processing helix chain 'Y' and resid 23 through 35 Processing helix chain 'Y' and resid 38 through 60 removed outlier: 4.237A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain '6' and resid 26 through 38 removed outlier: 3.764A pdb=" N PHE 6 30 " --> pdb=" O ASP 6 26 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU 6 33 " --> pdb=" O GLU 6 29 " (cutoff:3.500A) Processing helix chain '6' and resid 59 through 74 Processing helix chain '6' and resid 85 through 96 Processing helix chain '6' and resid 102 through 115 Processing helix chain '6' and resid 117 through 135 Processing helix chain '6' and resid 135 through 148 removed outlier: 3.514A pdb=" N GLY 6 139 " --> pdb=" O ARG 6 135 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS 6 142 " --> pdb=" O ARG 6 138 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU 6 143 " --> pdb=" O GLY 6 139 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN 6 146 " --> pdb=" O HIS 6 142 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 193 Processing helix chain '6' and resid 209 through 219 Processing helix chain '6' and resid 260 through 271 Processing helix chain '6' and resid 272 through 277 Processing helix chain '6' and resid 290 through 305 removed outlier: 4.090A pdb=" N ASN 6 294 " --> pdb=" O ARG 6 290 " (cutoff:3.500A) Processing helix chain '6' and resid 318 through 323 Processing helix chain '6' and resid 349 through 361 Processing helix chain '6' and resid 376 through 388 removed outlier: 3.906A pdb=" N ALA 6 388 " --> pdb=" O TYR 6 384 " (cutoff:3.500A) Processing helix chain '6' and resid 395 through 399 removed outlier: 3.563A pdb=" N GLY 6 398 " --> pdb=" O GLU 6 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER 6 399 " --> pdb=" O GLU 6 396 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 395 through 399' Processing helix chain '6' and resid 406 through 415 Processing helix chain 'x' and resid 5 through 10 Processing helix chain 'x' and resid 27 through 46 Processing helix chain 'x' and resid 71 through 77 removed outlier: 4.105A pdb=" N VAL x 75 " --> pdb=" O ARG x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 80 through 95 Processing helix chain 'x' and resid 111 through 125 Processing helix chain 'x' and resid 128 through 144 Processing helix chain 'f' and resid 19 through 30 Processing helix chain 'f' and resid 34 through 54 Processing helix chain 'f' and resid 56 through 69 Processing helix chain 'f' and resid 91 through 110 Processing helix chain 'f' and resid 114 through 128 Processing helix chain 'f' and resid 131 through 147 Processing helix chain 'h' and resid 34 through 39 removed outlier: 3.720A pdb=" N GLY h 39 " --> pdb=" O GLU h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 43 through 54 Proline residue: h 50 - end of helix removed outlier: 4.209A pdb=" N VAL h 54 " --> pdb=" O PRO h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 90 Processing helix chain 'h' and resid 93 through 101 Processing helix chain 'i' and resid 14 through 33 Processing helix chain 'i' and resid 80 through 87 Processing helix chain 'l' and resid 13 through 21 Processing helix chain 'l' and resid 25 through 37 removed outlier: 4.042A pdb=" N SER l 29 " --> pdb=" O GLY l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 62 Processing helix chain 'l' and resid 66 through 83 Processing helix chain 'l' and resid 84 through 92 removed outlier: 4.255A pdb=" N LEU l 88 " --> pdb=" O CYS l 84 " (cutoff:3.500A) Processing helix chain 'l' and resid 105 through 110 Processing helix chain 'm' and resid 2 through 18 removed outlier: 3.625A pdb=" N LYS m 6 " --> pdb=" O LYS m 2 " (cutoff:3.500A) Processing helix chain 'm' and resid 22 through 32 Processing helix chain 'm' and resid 42 through 51 Processing helix chain 'm' and resid 52 through 60 Proline residue: m 57 - end of helix Processing helix chain 'm' and resid 81 through 91 Processing helix chain 'r' and resid 11 through 25 Processing helix chain 'r' and resid 40 through 44 Processing helix chain 'r' and resid 70 through 74 removed outlier: 3.554A pdb=" N PHE r 73 " --> pdb=" O LEU r 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 23 through 30 Proline residue: w 28 - end of helix Processing helix chain 'w' and resid 41 through 59 Proline residue: w 47 - end of helix Processing helix chain 'w' and resid 75 through 80 Processing helix chain 'w' and resid 102 through 118 removed outlier: 4.126A pdb=" N GLN w 108 " --> pdb=" O LYS w 104 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 148 removed outlier: 4.041A pdb=" N MET w 135 " --> pdb=" O LYS w 131 " (cutoff:3.500A) Processing helix chain 'w' and resid 149 through 154 Processing helix chain 'w' and resid 168 through 179 removed outlier: 3.550A pdb=" N ILE w 172 " --> pdb=" O GLU w 168 " (cutoff:3.500A) Processing helix chain 'w' and resid 205 through 218 Processing helix chain 'c' and resid 6 through 15 removed outlier: 4.037A pdb=" N LEU c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 42 removed outlier: 4.571A pdb=" N ALA c 42 " --> pdb=" O GLN c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 65 Processing helix chain 'c' and resid 67 through 81 Processing helix chain 'c' and resid 84 through 96 Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 109 through 119 Processing helix chain 'c' and resid 151 through 164 removed outlier: 3.698A pdb=" N GLN c 163 " --> pdb=" O GLU c 159 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 191 Processing helix chain 'c' and resid 195 through 205 removed outlier: 3.980A pdb=" N ILE c 199 " --> pdb=" O ASN c 195 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 68 Processing helix chain 'd' and resid 110 through 118 Processing helix chain 'd' and resid 131 through 145 removed outlier: 4.911A pdb=" N ARG d 137 " --> pdb=" O ILE d 133 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE d 140 " --> pdb=" O VAL d 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'e' and resid 12 through 16 removed outlier: 4.922A pdb=" N GLU e 16 " --> pdb=" O ASP e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 17 through 32 Processing helix chain 'e' and resid 67 through 81 Processing helix chain 'g' and resid 4 through 19 Processing helix chain 'g' and resid 29 through 43 Processing helix chain 'g' and resid 94 through 98 Processing helix chain 'g' and resid 112 through 119 Processing helix chain 'j' and resid 52 through 56 removed outlier: 3.720A pdb=" N ARG j 55 " --> pdb=" O ARG j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 73 removed outlier: 3.710A pdb=" N ALA j 62 " --> pdb=" O THR j 58 " (cutoff:3.500A) Processing helix chain 'j' and resid 91 through 103 Processing helix chain 'k' and resid 2 through 9 Processing helix chain 'n' and resid 3 through 15 Processing helix chain 'n' and resid 23 through 44 removed outlier: 3.877A pdb=" N GLY n 40 " --> pdb=" O ASN n 36 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU n 44 " --> pdb=" O GLY n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 73 removed outlier: 3.733A pdb=" N GLY n 54 " --> pdb=" O HIS n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 73 through 85 Processing helix chain 'o' and resid 53 through 64 Processing helix chain 'o' and resid 68 through 78 Processing helix chain 'p' and resid 48 through 51 Processing helix chain 'q' and resid 24 through 29 Processing helix chain 'q' and resid 40 through 45 Processing helix chain 'q' and resid 47 through 64 Processing helix chain 's' and resid 4 through 41 removed outlier: 3.748A pdb=" N LYS s 8 " --> pdb=" O LYS s 4 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 64 Proline residue: s 55 - end of helix Processing helix chain 's' and resid 68 through 86 Processing helix chain 't' and resid 22 through 33 removed outlier: 4.427A pdb=" N GLY t 26 " --> pdb=" O CYS t 22 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG t 33 " --> pdb=" O ALA t 29 " (cutoff:3.500A) Processing helix chain 't' and resid 38 through 52 removed outlier: 4.476A pdb=" N THR t 42 " --> pdb=" O GLU t 38 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain '1' and resid 19 through 24 Processing sheet with id=AA3, first strand: chain '3' and resid 14 through 15 Processing sheet with id=AA4, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AA6, first strand: chain 'C' and resid 75 through 81 removed outlier: 5.379A pdb=" N VAL C 77 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU C 94 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 92 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AA8, first strand: chain 'C' and resid 143 through 144 removed outlier: 6.562A pdb=" N VAL C 143 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 170 through 174 removed outlier: 3.536A pdb=" N ARG C 268 " --> pdb=" O MET C 180 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS C 182 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE C 266 " --> pdb=" O LYS C 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 14 removed outlier: 5.866A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N MET D 11 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL D 24 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG D 13 " --> pdb=" O ILE D 22 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE D 22 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 38 removed outlier: 5.420A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 117 through 119 removed outlier: 3.510A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB6, first strand: chain 'F' and resid 65 through 67 Processing sheet with id=AB7, first strand: chain 'G' and resid 15 through 19 removed outlier: 7.554A pdb=" N ILE G 23 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG G 34 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 40 through 44 Processing sheet with id=AB9, first strand: chain 'G' and resid 86 through 87 removed outlier: 7.383A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.525A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.690A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'K' and resid 6 through 9 removed outlier: 6.799A pdb=" N LYS K 39 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL K 23 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE K 37 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA K 82 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N CYS K 83 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN K 8 " --> pdb=" O CYS K 83 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU K 85 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 68 through 69 removed outlier: 3.780A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 9.612A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 74 through 77 Processing sheet with id=AC7, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AC8, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.671A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 39 through 42 Processing sheet with id=AD1, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.172A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 47 through 52 removed outlier: 6.525A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER O 52 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE O 35 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.631A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.541A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.552A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'S' and resid 6 through 10 removed outlier: 5.513A pdb=" N LYS S 6 " --> pdb=" O VAL S 105 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL S 105 " --> pdb=" O LYS S 6 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AD8, first strand: chain 'T' and resid 11 through 13 removed outlier: 6.758A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 64 through 65 removed outlier: 3.756A pdb=" N LYS U 32 " --> pdb=" O LEU U 28 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN U 26 " --> pdb=" O ILE U 34 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'U' and resid 40 through 45 removed outlier: 3.524A pdb=" N GLY U 56 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 82 through 84 Processing sheet with id=AE3, first strand: chain 'V' and resid 3 through 5 removed outlier: 6.382A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.594A pdb=" N ARG W 76 " --> pdb=" O LYS W 71 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N PHE W 44 " --> pdb=" O ILE W 79 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N ILE W 81 " --> pdb=" O PHE W 44 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 32 through 34 removed outlier: 6.651A pdb=" N LEU W 58 " --> pdb=" O GLY W 33 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 12 through 15 Processing sheet with id=AE7, first strand: chain 'X' and resid 33 through 39 Processing sheet with id=AE8, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AE9, first strand: chain '6' and resid 78 through 79 removed outlier: 6.557A pdb=" N VAL 6 78 " --> pdb=" O ILE 6 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain '6' and resid 236 through 240 removed outlier: 4.247A pdb=" N ARG 6 237 " --> pdb=" O LEU 6 249 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU 6 249 " --> pdb=" O ARG 6 237 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR 6 247 " --> pdb=" O ILE 6 239 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N THR 6 199 " --> pdb=" O LEU 6 279 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU 6 281 " --> pdb=" O THR 6 199 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N SER 6 201 " --> pdb=" O LEU 6 281 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL 6 283 " --> pdb=" O SER 6 201 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL 6 203 " --> pdb=" O VAL 6 283 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU 6 280 " --> pdb=" O LEU 6 313 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL 6 315 " --> pdb=" O LEU 6 280 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N HIS 6 282 " --> pdb=" O VAL 6 315 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'x' and resid 19 through 20 removed outlier: 6.671A pdb=" N HIS x 68 " --> pdb=" O SER x 52 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE x 54 " --> pdb=" O THR x 66 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N THR x 66 " --> pdb=" O ILE x 54 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE x 56 " --> pdb=" O ARG x 64 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ARG x 64 " --> pdb=" O ILE x 56 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'x' and resid 164 through 170 removed outlier: 4.735A pdb=" N VAL x 194 " --> pdb=" O THR x 190 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR x 190 " --> pdb=" O VAL x 194 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N GLY x 196 " --> pdb=" O ALA x 188 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA x 188 " --> pdb=" O GLY x 196 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LYS x 198 " --> pdb=" O SER x 186 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N SER x 186 " --> pdb=" O LYS x 198 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TRP x 200 " --> pdb=" O ASN x 184 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ASN x 184 " --> pdb=" O TRP x 200 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE x 202 " --> pdb=" O ASP x 182 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP x 182 " --> pdb=" O PHE x 202 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY x 204 " --> pdb=" O ASP x 180 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'f' and resid 72 through 75 Processing sheet with id=AF5, first strand: chain 'h' and resid 10 through 11 Processing sheet with id=AF6, first strand: chain 'h' and resid 18 through 22 Processing sheet with id=AF7, first strand: chain 'h' and resid 28 through 29 Processing sheet with id=AF8, first strand: chain 'i' and resid 40 through 52 removed outlier: 3.504A pdb=" N LEU i 42 " --> pdb=" O LEU i 71 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU i 71 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR i 44 " --> pdb=" O THR i 69 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR i 69 " --> pdb=" O THR i 44 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS i 46 " --> pdb=" O ILE i 67 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE i 67 " --> pdb=" O LYS i 46 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG i 48 " --> pdb=" O TYR i 65 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR i 65 " --> pdb=" O ARG i 48 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR i 50 " --> pdb=" O ASP i 63 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP i 63 " --> pdb=" O THR i 50 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'i' and resid 40 through 52 removed outlier: 3.504A pdb=" N LEU i 42 " --> pdb=" O LEU i 71 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU i 71 " --> pdb=" O LEU i 42 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR i 44 " --> pdb=" O THR i 69 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N THR i 69 " --> pdb=" O THR i 44 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS i 46 " --> pdb=" O ILE i 67 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE i 67 " --> pdb=" O LYS i 46 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG i 48 " --> pdb=" O TYR i 65 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR i 65 " --> pdb=" O ARG i 48 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR i 50 " --> pdb=" O ASP i 63 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ASP i 63 " --> pdb=" O THR i 50 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'm' and resid 73 through 74 removed outlier: 3.550A pdb=" N LEU m 79 " --> pdb=" O LEU m 74 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'r' and resid 30 through 32 removed outlier: 3.696A pdb=" N ASN r 52 " --> pdb=" O GLN r 55 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN r 55 " --> pdb=" O ASN r 52 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'u' and resid 158 through 160 removed outlier: 3.633A pdb=" N VAL u 160 " --> pdb=" O VAL u 171 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'u' and resid 163 through 164 Processing sheet with id=AG5, first strand: chain 'w' and resid 160 through 162 removed outlier: 6.461A pdb=" N LEU w 160 " --> pdb=" O PHE w 183 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE w 185 " --> pdb=" O LEU w 160 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL w 162 " --> pdb=" O ILE w 185 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL w 182 " --> pdb=" O PHE w 197 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE w 199 " --> pdb=" O VAL w 182 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ALA w 184 " --> pdb=" O ILE w 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'c' and resid 127 through 128 Processing sheet with id=AG7, first strand: chain 'd' and resid 11 through 21 removed outlier: 5.336A pdb=" N GLU d 12 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLY d 39 " --> pdb=" O GLU d 12 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU d 14 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL d 37 " --> pdb=" O LEU d 14 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA d 16 " --> pdb=" O LEU d 35 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 84 through 87 removed outlier: 6.679A pdb=" N ILE d 105 " --> pdb=" O ALA d 124 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ALA d 126 " --> pdb=" O ILE d 105 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'e' and resid 2 through 4 Processing sheet with id=AH1, first strand: chain 'e' and resid 40 through 51 removed outlier: 5.025A pdb=" N ASP e 41 " --> pdb=" O LEU e 61 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU e 61 " --> pdb=" O ASP e 41 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS e 55 " --> pdb=" O LEU e 47 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG e 86 " --> pdb=" O MET e 9 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 23 through 27 removed outlier: 6.327A pdb=" N GLU g 57 " --> pdb=" O VAL g 50 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL g 50 " --> pdb=" O GLU g 57 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU g 59 " --> pdb=" O PHE g 48 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE g 48 " --> pdb=" O GLU g 59 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR g 61 " --> pdb=" O GLU g 46 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'g' and resid 73 through 76 Processing sheet with id=AH4, first strand: chain 'g' and resid 73 through 76 removed outlier: 5.801A pdb=" N ILE g 124 " --> pdb=" O SER g 104 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER g 104 " --> pdb=" O ILE g 124 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS g 126 " --> pdb=" O VAL g 102 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'j' and resid 40 through 45 removed outlier: 6.526A pdb=" N GLY j 18 " --> pdb=" O GLU j 82 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N MET j 84 " --> pdb=" O GLY j 18 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA j 20 " --> pdb=" O MET j 84 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS j 86 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE j 22 " --> pdb=" O LYS j 86 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU j 81 " --> pdb=" O ASN j 108 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N THR j 110 " --> pdb=" O LEU j 81 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL j 83 " --> pdb=" O THR j 110 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'k' and resid 38 through 39 removed outlier: 3.800A pdb=" N TYR k 94 " --> pdb=" O THR k 63 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N LEU k 80 " --> pdb=" O VAL k 97 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'o' and resid 50 through 51 removed outlier: 6.708A pdb=" N VAL o 19 " --> pdb=" O VAL o 36 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE o 38 " --> pdb=" O TYR o 17 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR o 17 " --> pdb=" O PHE o 38 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL o 2 " --> pdb=" O THR o 66 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'p' and resid 6 through 13 removed outlier: 16.474A pdb=" N THR p 6 " --> pdb=" O PHE p 27 " (cutoff:3.500A) removed outlier: 12.414A pdb=" N PHE p 27 " --> pdb=" O THR p 6 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN p 8 " --> pdb=" O GLU p 25 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU p 25 " --> pdb=" O GLN p 8 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL p 21 " --> pdb=" O VAL p 12 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N LYS p 70 " --> pdb=" O LYS p 42 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N HIS p 44 " --> pdb=" O LYS p 70 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP p 72 " --> pdb=" O HIS p 44 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N SER p 71 " --> pdb=" O CYS p 63 " (cutoff:3.500A) 1882 hydrogen bonds defined for protein. 5346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3716 hydrogen bonds 5872 hydrogen bond angles 0 basepair planarities 1468 basepair parallelities 2449 stacking parallelities Total time for adding SS restraints: 233.53 Time building geometry restraints manager: 65.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 16540 1.32 - 1.45: 71726 1.45 - 1.58: 59702 1.58 - 1.71: 8406 1.71 - 1.85: 262 Bond restraints: 156636 Sorted by residual: bond pdb=" N9 A B1916 " pdb=" C4 A B1916 " ideal model delta sigma weight residual 1.374 1.608 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C5 A B1916 " pdb=" C4 A B1916 " ideal model delta sigma weight residual 1.383 1.189 0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" N9 A B1916 " pdb=" C8 A B1916 " ideal model delta sigma weight residual 1.373 1.212 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N7 A B1916 " pdb=" C5 A B1916 " ideal model delta sigma weight residual 1.388 1.545 -0.157 2.00e-02 2.50e+03 6.16e+01 bond pdb=" N3 A B1916 " pdb=" C4 A B1916 " ideal model delta sigma weight residual 1.344 1.448 -0.104 2.00e-02 2.50e+03 2.73e+01 ... (remaining 156631 not shown) Histogram of bond angle deviations from ideal: 32.19 - 57.45: 2 57.45 - 82.71: 1 82.71 - 107.97: 41595 107.97 - 133.24: 192381 133.24 - 158.50: 114 Bond angle restraints: 234093 Sorted by residual: angle pdb=" N7 A B1916 " pdb=" C5 A B1916 " pdb=" C4 A B1916 " ideal model delta sigma weight residual 110.70 32.19 78.51 3.00e+00 1.11e-01 6.85e+02 angle pdb=" N9 A B1916 " pdb=" C8 A B1916 " pdb=" N7 A B1916 " ideal model delta sigma weight residual 113.80 46.37 67.43 3.00e+00 1.11e-01 5.05e+02 angle pdb=" N9 A B1916 " pdb=" C4 A B1916 " pdb=" C5 A B1916 " ideal model delta sigma weight residual 105.80 67.47 38.33 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C8 A B1916 " pdb=" N7 A B1916 " pdb=" C5 A B1916 " ideal model delta sigma weight residual 103.90 136.67 -32.77 3.00e+00 1.11e-01 1.19e+02 angle pdb=" N9 A B1916 " pdb=" C4 A B1916 " pdb=" N3 A B1916 " ideal model delta sigma weight residual 127.40 158.50 -31.10 3.00e+00 1.11e-01 1.07e+02 ... (remaining 234088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 86909 35.96 - 71.91: 12117 71.91 - 107.87: 1225 107.87 - 143.82: 21 143.82 - 179.78: 36 Dihedral angle restraints: 100308 sinusoidal: 83445 harmonic: 16863 Sorted by residual: dihedral pdb=" O4' C B2858 " pdb=" C1' C B2858 " pdb=" N1 C B2858 " pdb=" C2 C B2858 " ideal model delta sinusoidal sigma weight residual -160.00 15.27 -175.27 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U B2477 " pdb=" C1' U B2477 " pdb=" N1 U B2477 " pdb=" C2 U B2477 " ideal model delta sinusoidal sigma weight residual 200.00 26.86 173.14 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U B 652 " pdb=" C1' U B 652 " pdb=" N1 U B 652 " pdb=" C2 U B 652 " ideal model delta sinusoidal sigma weight residual 200.00 29.47 170.53 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 100305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 28581 0.117 - 0.234: 1191 0.234 - 0.352: 74 0.352 - 0.469: 16 0.469 - 0.586: 2 Chirality restraints: 29864 Sorted by residual: chirality pdb=" CB VAL V 72 " pdb=" CA VAL V 72 " pdb=" CG1 VAL V 72 " pdb=" CG2 VAL V 72 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.58e+00 chirality pdb=" CG LEU K 85 " pdb=" CB LEU K 85 " pdb=" CD1 LEU K 85 " pdb=" CD2 LEU K 85 " both_signs ideal model delta sigma weight residual False -2.59 -2.09 -0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" CB THR J 45 " pdb=" CA THR J 45 " pdb=" OG1 THR J 45 " pdb=" CG2 THR J 45 " both_signs ideal model delta sigma weight residual False 2.55 2.09 0.46 2.00e-01 2.50e+01 5.26e+00 ... (remaining 29861 not shown) Planarity restraints: 12746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS V 83 " -0.091 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO V 84 " 0.234 5.00e-02 4.00e+02 pdb=" CA PRO V 84 " -0.073 5.00e-02 4.00e+02 pdb=" CD PRO V 84 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG k 120 " 0.091 5.00e-02 4.00e+02 1.35e-01 2.91e+01 pdb=" N PRO k 121 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO k 121 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO k 121 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 137 " -0.024 2.00e-02 2.50e+03 4.81e-02 2.32e+01 pdb=" C ARG d 137 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG d 137 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA d 138 " -0.028 2.00e-02 2.50e+03 ... (remaining 12743 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 3862 2.63 - 3.20: 108818 3.20 - 3.77: 296115 3.77 - 4.33: 395535 4.33 - 4.90: 530319 Nonbonded interactions: 1334649 Sorted by model distance: nonbonded pdb=" N7 A B1916 " pdb=" N3 A B1916 " model vdw 2.065 2.560 nonbonded pdb=" O2 U B1680 " pdb=" O2' G B1763 " model vdw 2.111 2.440 nonbonded pdb=" OP1 A B1952 " pdb=" OG1 THR K 41 " model vdw 2.174 2.440 nonbonded pdb=" O THR i 80 " pdb=" OG1 THR i 83 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR l 27 " pdb=" O4' C v1328 " model vdw 2.220 2.440 ... (remaining 1334644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.180 Extract box with map and model: 14.040 Check model and map are aligned: 1.580 Set scattering table: 1.010 Process input model: 509.600 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 534.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4029 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 : 0.008 0.234 156636 Z= 0.469 Angle : 1.009 78.510 234093 Z= 0.495 Chirality : 0.055 0.586 29864 Planarity : 0.008 0.135 12746 Dihedral : 24.416 179.781 89426 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 0.72 % Allowed : 33.07 % Favored : 66.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.60 (0.10), residues: 5816 helix: -0.86 (0.10), residues: 1935 sheet: 0.16 (0.17), residues: 862 loop : -1.55 (0.10), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP 6 140 HIS 0.022 0.003 HIS i 56 PHE 0.038 0.004 PHE h 38 TYR 0.072 0.004 TYR 6 17 ARG 0.020 0.001 ARG l 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 461 time to evaluate : 5.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 MET cc_start: 0.0604 (mmp) cc_final: -0.1803 (mmp) REVERT: 6 1 MET cc_start: -0.0542 (mmt) cc_final: -0.1029 (mmt) REVERT: 6 406 MET cc_start: -0.2827 (mmt) cc_final: -0.3713 (mmt) REVERT: i 65 TYR cc_start: 0.6450 (m-80) cc_final: 0.5764 (m-10) REVERT: u 141 PHE cc_start: -0.1221 (OUTLIER) cc_final: -0.1777 (m-80) REVERT: e 94 HIS cc_start: 0.1253 (OUTLIER) cc_final: 0.0888 (m-70) REVERT: g 51 GLU cc_start: 0.5474 (mm-30) cc_final: 0.5115 (mm-30) REVERT: k 4 ASN cc_start: 0.5533 (t0) cc_final: 0.5302 (t0) outliers start: 35 outliers final: 5 residues processed: 491 average time/residue: 1.3310 time to fit residues: 1113.2828 Evaluate side-chains 408 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 401 time to evaluate : 5.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain l residue 29 SER Chi-restraints excluded: chain u residue 141 PHE Chi-restraints excluded: chain d residue 80 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 94 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 863 optimal weight: 3.9990 chunk 775 optimal weight: 0.9980 chunk 430 optimal weight: 1.9990 chunk 264 optimal weight: 20.0000 chunk 523 optimal weight: 0.9980 chunk 414 optimal weight: 20.0000 chunk 801 optimal weight: 0.9980 chunk 310 optimal weight: 5.9990 chunk 487 optimal weight: 2.9990 chunk 596 optimal weight: 0.9980 chunk 928 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 18 HIS 4 13 ASN 4 33 HIS C 43 ASN C 199 HIS ** C 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN G 127 GLN J 77 HIS K 2 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN R 91 GLN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 417 GLN x 99 GLN h 30 ASN h 49 GLN m 66 GLN w 35 ASN c 88 ASN c 119 HIS c 130 ASN ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 ASN j 118 ASN ** k 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 HIS n 39 GLN s 74 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4826 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.197 156636 Z= 0.227 Angle : 0.694 81.962 234093 Z= 0.342 Chirality : 0.036 0.281 29864 Planarity : 0.006 0.159 12746 Dihedral : 24.184 179.922 77739 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 4.40 % Allowed : 32.02 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.72 (0.10), residues: 5816 helix: 0.58 (0.11), residues: 1925 sheet: 0.04 (0.17), residues: 874 loop : -1.35 (0.10), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP M 64 HIS 0.011 0.002 HIS S 102 PHE 0.036 0.002 PHE 2 5 TYR 0.037 0.002 TYR J 16 ARG 0.017 0.001 ARG W 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 449 time to evaluate : 6.008 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: C 200 MET cc_start: 0.0507 (mmp) cc_final: -0.2070 (mmp) REVERT: J 118 MET cc_start: 0.3798 (mmt) cc_final: 0.3577 (mmt) REVERT: R 82 HIS cc_start: 0.3033 (OUTLIER) cc_final: 0.2804 (t-90) REVERT: W 25 PHE cc_start: 0.1035 (OUTLIER) cc_final: 0.0680 (m-10) REVERT: 6 1 MET cc_start: -0.0455 (mmt) cc_final: -0.0966 (mmt) REVERT: 6 406 MET cc_start: -0.3027 (mmt) cc_final: -0.3958 (mmt) REVERT: x 63 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5846 (tt) REVERT: x 74 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.6079 (mp) REVERT: f 67 ASN cc_start: 0.7097 (t0) cc_final: 0.6803 (t0) REVERT: f 132 THR cc_start: 0.6765 (m) cc_final: 0.6562 (m) REVERT: h 94 ARG cc_start: 0.7256 (tpp80) cc_final: 0.6694 (ttt180) REVERT: m 89 MET cc_start: 0.6447 (mmm) cc_final: 0.6043 (mmm) REVERT: g 51 GLU cc_start: 0.5258 (mm-30) cc_final: 0.5014 (mm-30) REVERT: j 110 THR cc_start: 0.6271 (OUTLIER) cc_final: 0.5938 (t) REVERT: o 6 LEU cc_start: 0.5876 (mp) cc_final: 0.5490 (mp) outliers start: 214 outliers final: 73 residues processed: 622 average time/residue: 1.4190 time to fit residues: 1537.1871 Evaluate side-chains 500 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 422 time to evaluate : 5.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 12 SER Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 111 LYS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain W residue 25 PHE Chi-restraints excluded: chain Z residue 53 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain x residue 44 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 74 ILE Chi-restraints excluded: chain x residue 75 VAL Chi-restraints excluded: chain x residue 118 SER Chi-restraints excluded: chain x residue 172 VAL Chi-restraints excluded: chain x residue 190 THR Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 71 ILE Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 6 ILE Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 29 SER Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain r residue 5 LYS Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 88 ASN Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain e residue 68 GLN Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain g residue 110 MET Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 76 HIS Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 78 THR Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain t residue 12 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 516 optimal weight: 5.9990 chunk 288 optimal weight: 7.9990 chunk 773 optimal weight: 2.9990 chunk 632 optimal weight: 7.9990 chunk 256 optimal weight: 7.9990 chunk 930 optimal weight: 5.9990 chunk 1005 optimal weight: 5.9990 chunk 828 optimal weight: 9.9990 chunk 922 optimal weight: 7.9990 chunk 317 optimal weight: 6.9990 chunk 746 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS C 141 HIS C 250 GLN D 134 HIS D 148 GLN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN G 21 GLN J 135 GLN O 104 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN R 6 GLN R 91 GLN S 9 HIS U 68 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 45 HIS Y 36 GLN Z 8 GLN 6 215 ASN 6 258 HIS x 24 ASN x 122 GLN x 175 HIS m 71 HIS ** w 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 189 ASN d 131 ASN ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 15 ASN ** k 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 71 HIS n 39 GLN ** o 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 GLN q 53 GLN s 19 HIS s 74 HIS s 81 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.9264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.251 156636 Z= 0.625 Angle : 1.179 82.364 234093 Z= 0.564 Chirality : 0.061 1.067 29864 Planarity : 0.009 0.213 12746 Dihedral : 24.484 179.606 77728 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.00 % Favored : 93.88 % Rotamer: Outliers : 7.90 % Allowed : 30.34 % Favored : 61.76 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.51 % Twisted General : 0.14 % 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: -1.71 (0.10), residues: 5816 helix: -0.54 (0.11), residues: 1925 sheet: -0.42 (0.17), residues: 881 loop : -1.76 (0.10), residues: 3010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.005 TRP T 80 HIS 0.073 0.004 HIS P 76 PHE 0.081 0.005 PHE w 68 TYR 0.051 0.004 TYR J 44 ARG 0.030 0.002 ARG k 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 495 time to evaluate : 6.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.8023 (mmm) cc_final: 0.7307 (mmm) REVERT: 4 2 LYS cc_start: 0.6891 (mttp) cc_final: 0.6348 (mttp) REVERT: C 131 MET cc_start: 0.2027 (mpp) cc_final: 0.0474 (mpp) REVERT: C 180 MET cc_start: 0.0968 (OUTLIER) cc_final: 0.0696 (mmp) REVERT: D 50 VAL cc_start: 0.6900 (OUTLIER) cc_final: 0.6623 (m) REVERT: D 177 VAL cc_start: 0.6069 (OUTLIER) cc_final: 0.4832 (m) REVERT: J 19 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6907 (t0) REVERT: J 92 MET cc_start: 0.7520 (tpp) cc_final: 0.6784 (ttm) REVERT: L 33 ARG cc_start: 0.7640 (mtt-85) cc_final: 0.7222 (mtt180) REVERT: L 55 MET cc_start: 0.7669 (tpp) cc_final: 0.7429 (tpt) REVERT: L 60 ARG cc_start: 0.8009 (ptt180) cc_final: 0.7685 (ptt180) REVERT: L 76 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6175 (pt0) REVERT: O 40 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6758 (tp) REVERT: R 32 THR cc_start: 0.6565 (OUTLIER) cc_final: 0.6303 (t) REVERT: S 20 VAL cc_start: 0.8056 (OUTLIER) cc_final: 0.7847 (m) REVERT: W 25 PHE cc_start: 0.3953 (OUTLIER) cc_final: 0.3604 (m-10) REVERT: 6 1 MET cc_start: -0.0139 (mmt) cc_final: -0.0639 (mmt) REVERT: 6 406 MET cc_start: -0.3239 (mmt) cc_final: -0.4565 (mmt) REVERT: x 9 ILE cc_start: 0.7753 (tp) cc_final: 0.7351 (tp) REVERT: x 10 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7654 (mtm-85) REVERT: x 63 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6744 (tt) REVERT: x 71 ARG cc_start: 0.7402 (ptm160) cc_final: 0.7053 (ptm160) REVERT: x 149 LYS cc_start: 0.7723 (ttpt) cc_final: 0.7453 (tttt) REVERT: f 57 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6672 (mt-10) REVERT: f 143 MET cc_start: 0.6005 (mmm) cc_final: 0.5791 (mmm) REVERT: h 10 ARG cc_start: 0.8179 (mtm-85) cc_final: 0.7846 (mtm-85) REVERT: h 56 MET cc_start: 0.2914 (tpp) cc_final: 0.2132 (tpp) REVERT: h 87 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6084 (mmp) REVERT: i 45 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.4880 (ttt180) REVERT: l 43 LYS cc_start: 0.4519 (OUTLIER) cc_final: 0.4244 (pttm) REVERT: l 69 ARG cc_start: 0.5545 (OUTLIER) cc_final: 0.3348 (ttp-170) REVERT: l 80 MET cc_start: 0.1292 (mmt) cc_final: 0.1028 (mmt) REVERT: m 58 SER cc_start: 0.7636 (OUTLIER) cc_final: 0.7346 (m) REVERT: u 141 PHE cc_start: -0.0991 (OUTLIER) cc_final: -0.1541 (m-80) REVERT: w 41 ASN cc_start: 0.5548 (OUTLIER) cc_final: 0.5346 (m-40) REVERT: c 55 ARG cc_start: 0.8107 (mmp80) cc_final: 0.7725 (mmp80) REVERT: c 61 ARG cc_start: 0.7428 (mmm-85) cc_final: 0.7179 (mtp180) REVERT: c 62 ARG cc_start: 0.7629 (mpt-90) cc_final: 0.7260 (mpt-90) REVERT: c 103 ARG cc_start: 0.7160 (mmm-85) cc_final: 0.6902 (mmm-85) REVERT: c 146 GLU cc_start: 0.5958 (OUTLIER) cc_final: 0.5735 (tm-30) REVERT: c 182 LYS cc_start: 0.6994 (ttpt) cc_final: 0.6794 (ttpt) REVERT: d 145 ASN cc_start: 0.6888 (m-40) cc_final: 0.6609 (m-40) REVERT: d 147 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6839 (p0) REVERT: d 155 LYS cc_start: 0.7755 (pttp) cc_final: 0.7524 (pttp) REVERT: e 21 MET cc_start: 0.7811 (mmt) cc_final: 0.7588 (mtp) REVERT: e 60 VAL cc_start: 0.8041 (OUTLIER) cc_final: 0.7697 (t) REVERT: g 9 MET cc_start: 0.7874 (ttp) cc_final: 0.7662 (ttm) REVERT: g 63 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7603 (mtmt) REVERT: g 70 VAL cc_start: 0.7541 (m) cc_final: 0.7278 (t) REVERT: g 95 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.6020 (mtt) REVERT: j 84 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.5963 (mmm) REVERT: j 121 ARG cc_start: 0.7704 (ptm160) cc_final: 0.7491 (ptm160) REVERT: k 30 ARG cc_start: 0.7053 (OUTLIER) cc_final: 0.6764 (ptt180) REVERT: k 61 GLU cc_start: 0.5504 (mp0) cc_final: 0.5205 (mp0) REVERT: k 98 ARG cc_start: 0.7476 (mtp180) cc_final: 0.7261 (mmm160) REVERT: n 9 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7976 (mtpp) REVERT: n 73 ASP cc_start: 0.5990 (OUTLIER) cc_final: 0.5668 (p0) REVERT: t 38 GLU cc_start: 0.5087 (OUTLIER) cc_final: 0.4799 (pt0) outliers start: 384 outliers final: 147 residues processed: 814 average time/residue: 1.3045 time to fit residues: 1802.6138 Evaluate side-chains 649 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 474 time to evaluate : 5.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 32 LYS Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 20 ASP Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 TRP Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 125 SER Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 31 GLU Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 19 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 76 GLU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 75 PHE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain T residue 15 HIS Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 97 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 25 PHE Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 50 VAL Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 95 LEU Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 258 HIS Chi-restraints excluded: chain 6 residue 298 VAL Chi-restraints excluded: chain x residue 10 ARG Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 92 ASP Chi-restraints excluded: chain x residue 96 VAL Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 135 LYS Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 87 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 6 ILE Chi-restraints excluded: chain i residue 26 VAL Chi-restraints excluded: chain i residue 45 ARG Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain l residue 22 TYR Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 27 THR Chi-restraints excluded: chain l residue 29 SER Chi-restraints excluded: chain l residue 38 ILE Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 91 ARG Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 64 CYS Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain u residue 141 PHE Chi-restraints excluded: chain w residue 30 ILE Chi-restraints excluded: chain w residue 41 ASN Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 89 PHE Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain w residue 188 THR Chi-restraints excluded: chain w residue 195 VAL Chi-restraints excluded: chain w residue 211 LEU Chi-restraints excluded: chain c residue 11 SER Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 116 LEU Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain c residue 147 LYS Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 6 ILE Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain g residue 63 LYS Chi-restraints excluded: chain g residue 95 MET Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain j residue 26 PHE Chi-restraints excluded: chain j residue 29 THR Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 76 HIS Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 73 ASP Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 15 LYS Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 44 THR Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 42 ASP Chi-restraints excluded: chain s residue 53 MET Chi-restraints excluded: chain s residue 81 GLN Chi-restraints excluded: chain t residue 38 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 919 optimal weight: 7.9990 chunk 699 optimal weight: 0.9990 chunk 483 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 444 optimal weight: 4.9990 chunk 624 optimal weight: 10.0000 chunk 934 optimal weight: 3.9990 chunk 988 optimal weight: 3.9990 chunk 487 optimal weight: 0.7980 chunk 885 optimal weight: 7.9990 chunk 266 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 162 GLN D 36 GLN D 130 GLN J 77 HIS ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN Q 19 GLN ** R 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 ASN V 44 HIS Y 39 GLN Z 19 HIS 6 258 HIS w 92 ASN d 76 ASN d 81 GLN ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 HIS s 2 ASN s 81 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.9471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.182 156636 Z= 0.215 Angle : 0.681 82.874 234093 Z= 0.335 Chirality : 0.038 0.381 29864 Planarity : 0.005 0.068 12746 Dihedral : 24.009 180.000 77728 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.46 % Rotamer: Outliers : 4.32 % Allowed : 32.81 % Favored : 62.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.10), residues: 5816 helix: 0.51 (0.12), residues: 1946 sheet: -0.15 (0.17), residues: 875 loop : -1.60 (0.10), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 64 HIS 0.050 0.002 HIS 6 258 PHE 0.030 0.002 PHE 6 267 TYR 0.017 0.002 TYR l 22 ARG 0.034 0.001 ARG l 2 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 449 time to evaluate : 6.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 22 MET cc_start: 0.7769 (mmm) cc_final: 0.7260 (mmm) REVERT: C 162 GLN cc_start: -0.0132 (OUTLIER) cc_final: -0.0362 (tm130) REVERT: C 254 LYS cc_start: 0.6725 (tptp) cc_final: 0.6002 (tptp) REVERT: D 11 MET cc_start: 0.7351 (mtm) cc_final: 0.7111 (mtm) REVERT: D 28 GLU cc_start: 0.6508 (tt0) cc_final: 0.6074 (tt0) REVERT: D 168 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5331 (pp20) REVERT: D 202 ILE cc_start: 0.7803 (pt) cc_final: 0.7565 (mt) REVERT: E 19 PHE cc_start: 0.6829 (m-10) cc_final: 0.6464 (m-80) REVERT: F 144 LYS cc_start: 0.2514 (OUTLIER) cc_final: 0.1093 (mttp) REVERT: L 55 MET cc_start: 0.7611 (tpp) cc_final: 0.7390 (tpt) REVERT: N 73 ASN cc_start: 0.7475 (t0) cc_final: 0.7256 (t0) REVERT: N 90 ARG cc_start: 0.7808 (ttt90) cc_final: 0.7525 (mtt-85) REVERT: P 23 ASP cc_start: 0.6803 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: Q 28 SER cc_start: 0.7743 (t) cc_final: 0.7498 (p) REVERT: R 64 VAL cc_start: 0.8022 (OUTLIER) cc_final: 0.7776 (p) REVERT: U 61 GLU cc_start: 0.6105 (OUTLIER) cc_final: 0.5754 (mm-30) REVERT: W 25 PHE cc_start: 0.3745 (OUTLIER) cc_final: 0.3260 (m-10) REVERT: X 36 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6193 (mtp85) REVERT: Y 27 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6541 (p0) REVERT: Y 34 SER cc_start: 0.7846 (t) cc_final: 0.7428 (m) REVERT: 6 406 MET cc_start: -0.3397 (mmt) cc_final: -0.4559 (mmt) REVERT: x 9 ILE cc_start: 0.7615 (tp) cc_final: 0.7238 (tp) REVERT: x 10 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7404 (mtm-85) REVERT: x 63 ILE cc_start: 0.6934 (OUTLIER) cc_final: 0.6645 (tt) REVERT: x 71 ARG cc_start: 0.7357 (ptm160) cc_final: 0.7116 (ptm160) REVERT: f 68 VAL cc_start: 0.7907 (t) cc_final: 0.7676 (t) REVERT: h 6 TYR cc_start: 0.3550 (p90) cc_final: 0.3313 (p90) REVERT: h 10 ARG cc_start: 0.8188 (mtm-85) cc_final: 0.7789 (mtm-85) REVERT: h 56 MET cc_start: 0.2806 (tpp) cc_final: 0.2180 (tpp) REVERT: h 87 MET cc_start: 0.7023 (mmt) cc_final: 0.6794 (mmp) REVERT: h 91 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5689 (mm-30) REVERT: i 53 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7857 (pt) REVERT: m 58 SER cc_start: 0.7607 (OUTLIER) cc_final: 0.7196 (m) REVERT: w 41 ASN cc_start: 0.5368 (OUTLIER) cc_final: 0.5142 (m-40) REVERT: c 55 ARG cc_start: 0.7987 (mmp80) cc_final: 0.7681 (mmp80) REVERT: c 62 ARG cc_start: 0.7733 (mpt-90) cc_final: 0.7319 (mtt-85) REVERT: c 146 GLU cc_start: 0.6101 (OUTLIER) cc_final: 0.5885 (tm-30) REVERT: d 150 GLU cc_start: 0.6747 (mp0) cc_final: 0.6282 (mp0) REVERT: d 151 MET cc_start: 0.7136 (ptp) cc_final: 0.6860 (ptt) REVERT: d 155 LYS cc_start: 0.7698 (pttp) cc_final: 0.7475 (pttp) REVERT: e 60 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7591 (t) REVERT: j 110 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8122 (p) REVERT: k 69 GLU cc_start: 0.5726 (OUTLIER) cc_final: 0.5368 (mp0) REVERT: n 73 ASP cc_start: 0.6125 (OUTLIER) cc_final: 0.5864 (p0) REVERT: q 72 ARG cc_start: 0.5594 (OUTLIER) cc_final: 0.5321 (mtt90) outliers start: 210 outliers final: 97 residues processed: 624 average time/residue: 1.3309 time to fit residues: 1411.3685 Evaluate side-chains 550 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 433 time to evaluate : 6.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain C residue 180 MET Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 125 TRP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 98 TYR Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 25 PHE Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 17 TYR Chi-restraints excluded: chain 6 residue 36 SER Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 95 LEU Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 258 HIS Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 76 ILE Chi-restraints excluded: chain x residue 92 ASP Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 91 GLU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 53 ILE Chi-restraints excluded: chain i residue 100 ILE Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 29 SER Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 41 ASN Chi-restraints excluded: chain w residue 89 PHE Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain w residue 211 LEU Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain j residue 26 PHE Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain n residue 73 ASP Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 72 ARG Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 53 MET Chi-restraints excluded: chain s residue 81 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 823 optimal weight: 1.9990 chunk 561 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 736 optimal weight: 2.9990 chunk 407 optimal weight: 7.9990 chunk 843 optimal weight: 5.9990 chunk 683 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 504 optimal weight: 4.9990 chunk 887 optimal weight: 7.9990 chunk 249 optimal weight: 100.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 30 HIS D 67 HIS D 130 GLN D 134 HIS L 38 GLN M 13 HIS N 3 HIS ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 128 GLN 6 258 HIS f 67 ASN f 129 ASN h 74 GLN w 93 HIS c 130 ASN ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 1.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.182 156636 Z= 0.345 Angle : 0.754 83.325 234093 Z= 0.369 Chirality : 0.043 0.545 29864 Planarity : 0.006 0.121 12746 Dihedral : 23.822 179.988 77728 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.02 % Rotamer: Outliers : 5.17 % Allowed : 32.33 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.96 (0.11), residues: 5816 helix: 0.53 (0.12), residues: 1939 sheet: -0.32 (0.17), residues: 917 loop : -1.56 (0.10), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP T 80 HIS 0.018 0.002 HIS 6 258 PHE 0.026 0.002 PHE Q 78 TYR 0.019 0.002 TYR g 85 ARG 0.017 0.001 ARG N 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 466 time to evaluate : 6.219 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: 2 22 MET cc_start: 0.7723 (mmm) cc_final: 0.7216 (mmm) REVERT: 2 39 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7472 (mtt-85) REVERT: C 131 MET cc_start: 0.3528 (mpp) cc_final: 0.1936 (mpp) REVERT: D 125 TRP cc_start: 0.7052 (OUTLIER) cc_final: 0.6309 (m100) REVERT: D 168 GLU cc_start: 0.6379 (OUTLIER) cc_final: 0.6073 (pp20) REVERT: E 95 LYS cc_start: 0.7655 (tttt) cc_final: 0.7450 (tttp) REVERT: F 144 LYS cc_start: 0.2357 (OUTLIER) cc_final: 0.1065 (mttp) REVERT: G 138 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.5477 (tt0) REVERT: J 7 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7502 (mttp) REVERT: J 14 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6933 (m-30) REVERT: J 45 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7319 (p) REVERT: K 40 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7230 (tt) REVERT: L 55 MET cc_start: 0.7470 (tpp) cc_final: 0.7231 (tpt) REVERT: N 118 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7129 (ttp-110) REVERT: P 23 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6990 (m-30) REVERT: P 73 PHE cc_start: 0.6390 (OUTLIER) cc_final: 0.5819 (p90) REVERT: Q 71 ASN cc_start: 0.7844 (m110) cc_final: 0.7572 (m110) REVERT: T 33 LYS cc_start: 0.8050 (mtpt) cc_final: 0.7840 (ttpt) REVERT: W 25 PHE cc_start: 0.4349 (OUTLIER) cc_final: 0.4102 (m-10) REVERT: Y 27 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6833 (p0) REVERT: Y 34 SER cc_start: 0.8247 (t) cc_final: 0.7790 (m) REVERT: 6 24 MET cc_start: 0.4741 (tpt) cc_final: 0.4219 (tpt) REVERT: 6 259 LEU cc_start: 0.5233 (tp) cc_final: 0.4955 (tp) REVERT: 6 406 MET cc_start: -0.3161 (mmt) cc_final: -0.4559 (mmt) REVERT: x 9 ILE cc_start: 0.7649 (tp) cc_final: 0.7417 (tp) REVERT: x 71 ARG cc_start: 0.7369 (ptm160) cc_final: 0.7116 (ptm160) REVERT: x 130 ARG cc_start: 0.6890 (OUTLIER) cc_final: 0.6523 (mmp80) REVERT: f 57 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6542 (mt-10) REVERT: f 68 VAL cc_start: 0.7990 (t) cc_final: 0.7757 (t) REVERT: f 101 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7408 (ttm170) REVERT: h 10 ARG cc_start: 0.8221 (mtm-85) cc_final: 0.7585 (mtt90) REVERT: i 53 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7854 (pt) REVERT: l 43 LYS cc_start: 0.4130 (OUTLIER) cc_final: 0.3792 (pttm) REVERT: l 69 ARG cc_start: 0.5326 (OUTLIER) cc_final: 0.3530 (ttp-110) REVERT: l 70 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.5121 (ttp80) REVERT: m 53 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.4655 (mtt-85) REVERT: m 58 SER cc_start: 0.7647 (t) cc_final: 0.7253 (m) REVERT: u 141 PHE cc_start: -0.1017 (OUTLIER) cc_final: -0.1669 (m-80) REVERT: w 8 MET cc_start: 0.3518 (OUTLIER) cc_final: 0.2967 (ppp) REVERT: w 65 LYS cc_start: 0.0725 (OUTLIER) cc_final: -0.1666 (mtpt) REVERT: c 25 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.4779 (ttm170) REVERT: c 52 VAL cc_start: 0.7911 (t) cc_final: 0.7607 (m) REVERT: c 146 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5916 (tm-30) REVERT: c 187 ARG cc_start: 0.6320 (tpt90) cc_final: 0.6034 (tpt-90) REVERT: d 146 MET cc_start: 0.7177 (tpp) cc_final: 0.6912 (ttm) REVERT: d 150 GLU cc_start: 0.6802 (mp0) cc_final: 0.6404 (mp0) REVERT: d 151 MET cc_start: 0.7352 (ptp) cc_final: 0.7118 (ptt) REVERT: d 155 LYS cc_start: 0.7740 (pttp) cc_final: 0.7525 (pttp) REVERT: e 65 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5606 (pp20) REVERT: e 91 ARG cc_start: 0.5364 (OUTLIER) cc_final: 0.3654 (tpt170) REVERT: j 110 THR cc_start: 0.8494 (OUTLIER) cc_final: 0.8209 (p) REVERT: k 69 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5888 (mp0) REVERT: n 44 GLU cc_start: 0.2286 (OUTLIER) cc_final: 0.0643 (pt0) REVERT: n 73 ASP cc_start: 0.6153 (OUTLIER) cc_final: 0.5886 (p0) REVERT: o 14 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.7303 (mtp180) REVERT: s 38 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.8040 (mt) REVERT: s 81 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.7011 (mt0) outliers start: 251 outliers final: 131 residues processed: 666 average time/residue: 1.3633 time to fit residues: 1520.0540 Evaluate side-chains 616 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 453 time to evaluate : 5.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 125 TRP Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 129 MET Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 8 GLU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain Q residue 83 LYS Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 25 PHE Chi-restraints excluded: chain W residue 66 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 95 LEU Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 26 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 130 ARG Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain f residue 57 GLU Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 115 VAL Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 53 ILE Chi-restraints excluded: chain i residue 74 VAL Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 29 SER Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 57 ASP Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 ARG Chi-restraints excluded: chain l residue 91 ARG Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain u residue 141 PHE Chi-restraints excluded: chain w residue 8 MET Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 19 THR Chi-restraints excluded: chain w residue 30 ILE Chi-restraints excluded: chain w residue 48 MET Chi-restraints excluded: chain w residue 65 LYS Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 89 PHE Chi-restraints excluded: chain w residue 91 VAL Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain c residue 25 ARG Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 116 LEU Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 73 ASP Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 72 ARG Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 53 MET Chi-restraints excluded: chain s residue 81 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 332 optimal weight: 2.9990 chunk 890 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 580 optimal weight: 2.9990 chunk 244 optimal weight: 220.0000 chunk 989 optimal weight: 5.9990 chunk 821 optimal weight: 5.9990 chunk 458 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 519 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 37 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 13 HIS M 97 GLN N 3 HIS ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN 6 258 HIS f 129 ASN d 76 ASN ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 1.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.180 156636 Z= 0.324 Angle : 0.688 83.388 234093 Z= 0.339 Chirality : 0.041 0.433 29864 Planarity : 0.005 0.082 12746 Dihedral : 23.732 179.623 77728 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.62 % Favored : 94.34 % Rotamer: Outliers : 4.67 % Allowed : 32.58 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.11), residues: 5816 helix: 0.72 (0.12), residues: 1938 sheet: -0.29 (0.17), residues: 894 loop : -1.56 (0.10), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP T 80 HIS 0.015 0.002 HIS 6 118 PHE 0.031 0.002 PHE w 68 TYR 0.018 0.002 TYR J 75 ARG 0.020 0.001 ARG f 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 472 time to evaluate : 6.065 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: 2 22 MET cc_start: 0.7661 (mmm) cc_final: 0.7256 (mmm) REVERT: 2 39 ARG cc_start: 0.7978 (mtt-85) cc_final: 0.7429 (mtt-85) REVERT: C 47 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7445 (mmm-85) REVERT: C 62 ARG cc_start: 0.8112 (mpt180) cc_final: 0.7579 (mtm-85) REVERT: C 149 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7228 (tttt) REVERT: D 109 VAL cc_start: 0.8220 (t) cc_final: 0.7994 (m) REVERT: D 168 GLU cc_start: 0.6439 (OUTLIER) cc_final: 0.6150 (pp20) REVERT: D 172 VAL cc_start: 0.7473 (m) cc_final: 0.7211 (t) REVERT: E 14 VAL cc_start: 0.7670 (m) cc_final: 0.7398 (p) REVERT: E 19 PHE cc_start: 0.7664 (m-10) cc_final: 0.7284 (m-80) REVERT: E 120 VAL cc_start: 0.7789 (m) cc_final: 0.7569 (p) REVERT: F 144 LYS cc_start: 0.2329 (OUTLIER) cc_final: 0.1208 (mttp) REVERT: G 138 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.5739 (tt0) REVERT: J 45 THR cc_start: 0.7545 (OUTLIER) cc_final: 0.7316 (p) REVERT: K 40 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7158 (tt) REVERT: L 60 ARG cc_start: 0.7736 (ptt180) cc_final: 0.7467 (ptt180) REVERT: L 96 LYS cc_start: 0.8295 (mttp) cc_final: 0.8080 (mttt) REVERT: N 98 LEU cc_start: 0.8102 (mp) cc_final: 0.7861 (mt) REVERT: N 118 ARG cc_start: 0.7426 (ttp80) cc_final: 0.7186 (ttp80) REVERT: P 23 ASP cc_start: 0.7489 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: Q 71 ASN cc_start: 0.7973 (m110) cc_final: 0.7670 (m110) REVERT: S 69 LEU cc_start: 0.7830 (mt) cc_final: 0.7580 (mp) REVERT: T 56 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.4968 (tp30) REVERT: U 61 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.6052 (mm-30) REVERT: Y 27 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6833 (p0) REVERT: Y 34 SER cc_start: 0.8233 (t) cc_final: 0.7939 (m) REVERT: x 9 ILE cc_start: 0.7642 (tp) cc_final: 0.7420 (tp) REVERT: x 71 ARG cc_start: 0.7332 (ptm160) cc_final: 0.7108 (ptm160) REVERT: f 67 ASN cc_start: 0.7524 (OUTLIER) cc_final: 0.7269 (m-40) REVERT: f 101 ARG cc_start: 0.7855 (ttp80) cc_final: 0.7335 (ttm170) REVERT: h 10 ARG cc_start: 0.8242 (mtm-85) cc_final: 0.7633 (mtt90) REVERT: i 53 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7867 (pt) REVERT: l 43 LYS cc_start: 0.4046 (OUTLIER) cc_final: 0.3785 (pttm) REVERT: l 69 ARG cc_start: 0.5272 (OUTLIER) cc_final: 0.3860 (ttp-110) REVERT: l 70 ARG cc_start: 0.5600 (OUTLIER) cc_final: 0.5302 (ttp80) REVERT: m 53 ARG cc_start: 0.5426 (OUTLIER) cc_final: 0.4725 (mtt-85) REVERT: m 58 SER cc_start: 0.7625 (t) cc_final: 0.7237 (m) REVERT: u 141 PHE cc_start: -0.1169 (OUTLIER) cc_final: -0.1635 (m-80) REVERT: w 8 MET cc_start: 0.3352 (OUTLIER) cc_final: 0.1966 (ppp) REVERT: w 65 LYS cc_start: 0.0476 (OUTLIER) cc_final: -0.1887 (mtpt) REVERT: c 25 ARG cc_start: 0.5454 (OUTLIER) cc_final: 0.4790 (ttm170) REVERT: c 62 ARG cc_start: 0.7866 (mpt-90) cc_final: 0.7447 (mtt180) REVERT: c 146 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5976 (tm-30) REVERT: d 146 MET cc_start: 0.7148 (tpp) cc_final: 0.6927 (ttm) REVERT: d 150 GLU cc_start: 0.6876 (mp0) cc_final: 0.6520 (mp0) REVERT: d 151 MET cc_start: 0.7356 (ptp) cc_final: 0.7089 (ptp) REVERT: d 155 LYS cc_start: 0.7738 (pttp) cc_final: 0.7527 (pttp) REVERT: e 1 MET cc_start: 0.5174 (tpp) cc_final: 0.4850 (tpp) REVERT: e 65 GLU cc_start: 0.6115 (OUTLIER) cc_final: 0.5726 (pp20) REVERT: g 116 ARG cc_start: 0.8210 (mtm-85) cc_final: 0.7982 (mtm180) REVERT: j 84 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6006 (mmm) REVERT: j 110 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8188 (p) REVERT: n 44 GLU cc_start: 0.2682 (OUTLIER) cc_final: 0.0953 (pt0) REVERT: n 73 ASP cc_start: 0.6052 (OUTLIER) cc_final: 0.5791 (p0) REVERT: o 14 ARG cc_start: 0.8314 (mtp-110) cc_final: 0.7313 (mtp180) REVERT: s 81 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6918 (mm-40) outliers start: 227 outliers final: 136 residues processed: 653 average time/residue: 1.5600 time to fit residues: 1706.0098 Evaluate side-chains 631 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 467 time to evaluate : 6.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 94 ASP Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 95 LEU Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 298 VAL Chi-restraints excluded: chain 6 residue 418 GLU Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 76 ILE Chi-restraints excluded: chain x residue 92 ASP Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 109 LYS Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 71 ILE Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 6 ILE Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 53 ILE Chi-restraints excluded: chain l residue 16 ILE Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 27 THR Chi-restraints excluded: chain l residue 29 SER Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 57 ASP Chi-restraints excluded: chain l residue 67 ASP Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 ARG Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain u residue 141 PHE Chi-restraints excluded: chain w residue 8 MET Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 19 THR Chi-restraints excluded: chain w residue 30 ILE Chi-restraints excluded: chain w residue 48 MET Chi-restraints excluded: chain w residue 65 LYS Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 89 PHE Chi-restraints excluded: chain w residue 91 VAL Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain c residue 25 ARG Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain d residue 76 ASN Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 73 ASP Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 72 ARG Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 53 MET Chi-restraints excluded: chain s residue 57 VAL Chi-restraints excluded: chain s residue 81 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 954 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 563 optimal weight: 4.9990 chunk 722 optimal weight: 50.0000 chunk 560 optimal weight: 9.9990 chunk 833 optimal weight: 2.9990 chunk 552 optimal weight: 3.9990 chunk 986 optimal weight: 10.0000 chunk 617 optimal weight: 6.9990 chunk 601 optimal weight: 40.0000 chunk 455 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 13 HIS N 3 HIS ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN Y 27 ASN ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 11 HIS ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 1.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.178 156636 Z= 0.483 Angle : 0.794 83.779 234093 Z= 0.388 Chirality : 0.048 0.590 29864 Planarity : 0.006 0.138 12746 Dihedral : 23.773 179.604 77728 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.72 % Favored : 93.24 % Rotamer: Outliers : 5.04 % Allowed : 32.27 % Favored : 62.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 5816 helix: 0.49 (0.11), residues: 1961 sheet: -0.46 (0.17), residues: 893 loop : -1.68 (0.10), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP T 80 HIS 0.013 0.002 HIS l 13 PHE 0.047 0.003 PHE W 25 TYR 0.024 0.002 TYR g 85 ARG 0.016 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 474 time to evaluate : 6.170 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: 2 39 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7523 (mtt-85) REVERT: 3 29 ARG cc_start: 0.8143 (mmt-90) cc_final: 0.7902 (mtp85) REVERT: C 47 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7509 (mmm-85) REVERT: D 28 GLU cc_start: 0.6592 (tt0) cc_final: 0.6192 (tt0) REVERT: D 109 VAL cc_start: 0.8299 (t) cc_final: 0.8026 (m) REVERT: D 168 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.6207 (pp20) REVERT: E 14 VAL cc_start: 0.7396 (m) cc_final: 0.7164 (p) REVERT: E 120 VAL cc_start: 0.8044 (m) cc_final: 0.7781 (p) REVERT: E 162 ARG cc_start: 0.7842 (ttm110) cc_final: 0.7592 (ttm-80) REVERT: F 144 LYS cc_start: 0.2655 (OUTLIER) cc_final: 0.1574 (mttp) REVERT: G 138 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6412 (tt0) REVERT: L 60 ARG cc_start: 0.7756 (ptt-90) cc_final: 0.7493 (ptt180) REVERT: N 98 LEU cc_start: 0.8266 (mp) cc_final: 0.7967 (mt) REVERT: N 118 ARG cc_start: 0.7346 (ttp80) cc_final: 0.7110 (ttp-110) REVERT: P 23 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7260 (m-30) REVERT: Q 71 ASN cc_start: 0.7931 (m110) cc_final: 0.7719 (m110) REVERT: S 69 LEU cc_start: 0.7941 (mt) cc_final: 0.7724 (mp) REVERT: T 56 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.4769 (tp30) REVERT: U 61 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6062 (mm-30) REVERT: Y 27 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6707 (p0) REVERT: x 9 ILE cc_start: 0.7651 (tp) cc_final: 0.7427 (tp) REVERT: x 71 ARG cc_start: 0.7339 (ptm160) cc_final: 0.7101 (ptm160) REVERT: f 101 ARG cc_start: 0.7881 (ttp80) cc_final: 0.7431 (ttm170) REVERT: h 10 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.7636 (mtt90) REVERT: h 91 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5682 (mm-30) REVERT: l 43 LYS cc_start: 0.3689 (OUTLIER) cc_final: 0.3334 (pttm) REVERT: l 69 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.3947 (ttp-110) REVERT: l 70 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5554 (ttp80) REVERT: m 53 ARG cc_start: 0.5509 (OUTLIER) cc_final: 0.4926 (mtt-85) REVERT: m 58 SER cc_start: 0.7598 (t) cc_final: 0.7260 (m) REVERT: u 141 PHE cc_start: -0.1105 (OUTLIER) cc_final: -0.1613 (m-80) REVERT: w 8 MET cc_start: 0.3970 (OUTLIER) cc_final: 0.2898 (ppp) REVERT: w 65 LYS cc_start: 0.0831 (OUTLIER) cc_final: 0.0354 (mtpt) REVERT: w 89 PHE cc_start: 0.0191 (OUTLIER) cc_final: -0.0657 (p90) REVERT: c 25 ARG cc_start: 0.5691 (OUTLIER) cc_final: 0.5066 (ttm170) REVERT: c 52 VAL cc_start: 0.7952 (t) cc_final: 0.7654 (m) REVERT: c 62 ARG cc_start: 0.7893 (mpt-90) cc_final: 0.7496 (mtt180) REVERT: c 146 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5967 (tm-30) REVERT: c 177 MET cc_start: 0.8275 (mtp) cc_final: 0.7992 (mtp) REVERT: d 150 GLU cc_start: 0.6923 (mp0) cc_final: 0.6587 (mp0) REVERT: d 151 MET cc_start: 0.7423 (ptp) cc_final: 0.7219 (ptp) REVERT: d 155 LYS cc_start: 0.7775 (pttp) cc_final: 0.7561 (pttp) REVERT: e 1 MET cc_start: 0.5244 (tpp) cc_final: 0.4938 (tpp) REVERT: e 65 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5726 (pp20) REVERT: e 91 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.3913 (tpt90) REVERT: j 84 MET cc_start: 0.6782 (OUTLIER) cc_final: 0.6118 (mmm) REVERT: j 110 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8176 (p) REVERT: n 44 GLU cc_start: 0.2815 (OUTLIER) cc_final: 0.1071 (pt0) REVERT: n 73 ASP cc_start: 0.6023 (OUTLIER) cc_final: 0.5765 (p0) REVERT: o 14 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.7301 (mtp180) outliers start: 245 outliers final: 167 residues processed: 671 average time/residue: 1.5371 time to fit residues: 1716.0862 Evaluate side-chains 657 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 465 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 99 PHE Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 69 ARG Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 61 GLU Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 95 LEU Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 160 LEU Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 284 ILE Chi-restraints excluded: chain 6 residue 298 VAL Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ARG Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 76 ILE Chi-restraints excluded: chain x residue 92 ASP Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 109 LYS Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 135 LYS Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 71 ILE Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 91 GLU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 6 ILE Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 27 THR Chi-restraints excluded: chain l residue 29 SER Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 57 ASP Chi-restraints excluded: chain l residue 67 ASP Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 70 ARG Chi-restraints excluded: chain m residue 27 LYS Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain u residue 141 PHE Chi-restraints excluded: chain w residue 8 MET Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 19 THR Chi-restraints excluded: chain w residue 30 ILE Chi-restraints excluded: chain w residue 48 MET Chi-restraints excluded: chain w residue 65 LYS Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 89 PHE Chi-restraints excluded: chain w residue 91 VAL Chi-restraints excluded: chain w residue 101 THR Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain c residue 25 ARG Chi-restraints excluded: chain c residue 43 ARG Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 116 LEU Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 59 VAL Chi-restraints excluded: chain n residue 73 ASP Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 72 ARG Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 53 MET Chi-restraints excluded: chain s residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 610 optimal weight: 10.0000 chunk 393 optimal weight: 3.9990 chunk 588 optimal weight: 5.9990 chunk 297 optimal weight: 5.9990 chunk 193 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 626 optimal weight: 8.9990 chunk 671 optimal weight: 7.9990 chunk 487 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 775 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN N 3 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 ASN f 67 ASN ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 ASN ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 1.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.178 156636 Z= 0.345 Angle : 0.700 83.613 234093 Z= 0.345 Chirality : 0.041 0.496 29864 Planarity : 0.005 0.114 12746 Dihedral : 23.708 179.666 77728 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.98 % Rotamer: Outliers : 4.73 % Allowed : 32.43 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.99 (0.10), residues: 5816 helix: 0.68 (0.12), residues: 1955 sheet: -0.45 (0.17), residues: 892 loop : -1.68 (0.10), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP T 80 HIS 0.018 0.002 HIS M 13 PHE 0.029 0.002 PHE w 68 TYR 0.019 0.002 TYR n 77 ARG 0.011 0.001 ARG Q 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 449 time to evaluate : 5.971 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: 3 29 ARG cc_start: 0.8109 (mmt-90) cc_final: 0.7840 (mtp85) REVERT: C 149 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7194 (tttt) REVERT: D 28 GLU cc_start: 0.6620 (tt0) cc_final: 0.6209 (tt0) REVERT: D 84 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6896 (mt) REVERT: D 109 VAL cc_start: 0.8260 (t) cc_final: 0.8033 (m) REVERT: D 141 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7493 (mtp85) REVERT: D 168 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6210 (pp20) REVERT: E 162 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7550 (ttm-80) REVERT: F 144 LYS cc_start: 0.2555 (OUTLIER) cc_final: 0.1495 (mttp) REVERT: G 138 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6391 (tt0) REVERT: J 7 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7521 (mttp) REVERT: K 40 ILE cc_start: 0.7392 (OUTLIER) cc_final: 0.7134 (tt) REVERT: L 60 ARG cc_start: 0.7742 (ptt180) cc_final: 0.7520 (ptt180) REVERT: L 96 LYS cc_start: 0.8362 (mttp) cc_final: 0.8134 (mttt) REVERT: L 132 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7826 (ttm110) REVERT: N 98 LEU cc_start: 0.8248 (mp) cc_final: 0.7956 (mt) REVERT: N 118 ARG cc_start: 0.7322 (ttp80) cc_final: 0.7107 (ttp-110) REVERT: S 69 LEU cc_start: 0.7889 (mt) cc_final: 0.7615 (mp) REVERT: T 56 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.4581 (tp30) REVERT: W 75 ASN cc_start: 0.6692 (m-40) cc_final: 0.6462 (m-40) REVERT: Y 27 ASN cc_start: 0.6863 (OUTLIER) cc_final: 0.6495 (p0) REVERT: Z 29 ARG cc_start: 0.7660 (mtt-85) cc_final: 0.7415 (mtt90) REVERT: 6 24 MET cc_start: 0.5283 (tpt) cc_final: 0.5013 (tpt) REVERT: 6 371 ARG cc_start: 0.4089 (OUTLIER) cc_final: 0.3864 (mmp80) REVERT: x 9 ILE cc_start: 0.7624 (tp) cc_final: 0.7403 (tp) REVERT: x 10 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7855 (mtt90) REVERT: x 71 ARG cc_start: 0.7326 (ptm160) cc_final: 0.7098 (ptm160) REVERT: f 68 VAL cc_start: 0.7986 (t) cc_final: 0.7722 (t) REVERT: f 101 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7401 (ttm170) REVERT: h 10 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7617 (mtt90) REVERT: h 91 GLU cc_start: 0.5867 (OUTLIER) cc_final: 0.5595 (mm-30) REVERT: l 43 LYS cc_start: 0.3852 (OUTLIER) cc_final: 0.3546 (pttm) REVERT: l 69 ARG cc_start: 0.5422 (OUTLIER) cc_final: 0.3912 (ttp-110) REVERT: m 53 ARG cc_start: 0.5425 (OUTLIER) cc_final: 0.4929 (mtt-85) REVERT: m 58 SER cc_start: 0.7582 (t) cc_final: 0.7240 (m) REVERT: u 141 PHE cc_start: -0.1121 (OUTLIER) cc_final: -0.1643 (m-80) REVERT: w 8 MET cc_start: 0.3808 (OUTLIER) cc_final: 0.2166 (ppp) REVERT: w 89 PHE cc_start: 0.0072 (OUTLIER) cc_final: -0.0745 (p90) REVERT: c 25 ARG cc_start: 0.5589 (OUTLIER) cc_final: 0.4976 (ttm170) REVERT: c 52 VAL cc_start: 0.7892 (t) cc_final: 0.7615 (m) REVERT: c 62 ARG cc_start: 0.7830 (mpt-90) cc_final: 0.7433 (mtt180) REVERT: c 146 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6020 (tm-30) REVERT: c 177 MET cc_start: 0.8286 (mtt) cc_final: 0.7895 (mtp) REVERT: d 150 GLU cc_start: 0.6894 (mp0) cc_final: 0.6535 (mp0) REVERT: d 155 LYS cc_start: 0.7747 (pttp) cc_final: 0.7524 (pttp) REVERT: e 1 MET cc_start: 0.5205 (tpp) cc_final: 0.4923 (tpp) REVERT: e 65 GLU cc_start: 0.6176 (OUTLIER) cc_final: 0.5703 (pp20) REVERT: j 84 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.5939 (mmm) REVERT: j 110 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8195 (p) REVERT: n 44 GLU cc_start: 0.2882 (OUTLIER) cc_final: 0.1159 (pt0) REVERT: n 73 ASP cc_start: 0.6042 (OUTLIER) cc_final: 0.5787 (p0) REVERT: o 14 ARG cc_start: 0.8295 (mtp-110) cc_final: 0.7284 (mtp180) REVERT: p 27 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7307 (m-80) outliers start: 230 outliers final: 162 residues processed: 637 average time/residue: 1.5150 time to fit residues: 1597.7635 Evaluate side-chains 633 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 445 time to evaluate : 6.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 36 SER Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 160 LEU Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 298 VAL Chi-restraints excluded: chain 6 residue 342 LEU Chi-restraints excluded: chain 6 residue 345 GLN Chi-restraints excluded: chain 6 residue 371 ARG Chi-restraints excluded: chain x residue 10 ARG Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 76 ILE Chi-restraints excluded: chain x residue 92 ASP Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 109 LYS Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 135 LYS Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 88 GLU Chi-restraints excluded: chain h residue 91 GLU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 27 THR Chi-restraints excluded: chain l residue 29 SER Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 57 ASP Chi-restraints excluded: chain l residue 67 ASP Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain u residue 141 PHE Chi-restraints excluded: chain w residue 8 MET Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 19 THR Chi-restraints excluded: chain w residue 30 ILE Chi-restraints excluded: chain w residue 48 MET Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 89 PHE Chi-restraints excluded: chain w residue 91 VAL Chi-restraints excluded: chain w residue 101 THR Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 178 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain c residue 25 ARG Chi-restraints excluded: chain c residue 43 ARG Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain j residue 118 ASN Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 63 THR Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 73 ASP Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 27 PHE Chi-restraints excluded: chain p residue 49 ASN Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 72 ARG Chi-restraints excluded: chain s residue 53 MET Chi-restraints excluded: chain s residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 896 optimal weight: 6.9990 chunk 944 optimal weight: 6.9990 chunk 861 optimal weight: 10.0000 chunk 918 optimal weight: 7.9990 chunk 553 optimal weight: 2.9990 chunk 400 optimal weight: 20.0000 chunk 721 optimal weight: 3.9990 chunk 281 optimal weight: 10.0000 chunk 830 optimal weight: 2.9990 chunk 869 optimal weight: 10.0000 chunk 915 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN L 38 GLN M 13 HIS M 22 GLN N 3 HIS ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN U 68 ASN 6 367 GLN f 67 ASN ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 169 HIS d 76 ASN ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 1.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.178 156636 Z= 0.458 Angle : 0.780 83.853 234093 Z= 0.382 Chirality : 0.047 0.591 29864 Planarity : 0.006 0.156 12746 Dihedral : 23.736 179.407 77728 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.05 % Favored : 92.92 % Rotamer: Outliers : 4.71 % Allowed : 32.68 % Favored : 62.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.10), residues: 5816 helix: 0.51 (0.11), residues: 1950 sheet: -0.51 (0.17), residues: 865 loop : -1.77 (0.10), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP T 80 HIS 0.014 0.002 HIS l 13 PHE 0.034 0.003 PHE w 68 TYR 0.023 0.002 TYR g 85 ARG 0.012 0.001 ARG 6 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 457 time to evaluate : 6.053 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: 3 29 ARG cc_start: 0.8154 (mmt-90) cc_final: 0.7892 (mtp85) REVERT: C 47 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7416 (mmm-85) REVERT: D 28 GLU cc_start: 0.6592 (tt0) cc_final: 0.6184 (tt0) REVERT: D 84 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7016 (mt) REVERT: D 109 VAL cc_start: 0.8284 (t) cc_final: 0.8032 (m) REVERT: E 114 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6508 (mtm180) REVERT: E 120 VAL cc_start: 0.8170 (m) cc_final: 0.7850 (p) REVERT: E 162 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7605 (ttm-80) REVERT: F 94 ARG cc_start: 0.5795 (OUTLIER) cc_final: 0.5386 (mmp-170) REVERT: F 144 LYS cc_start: 0.2677 (OUTLIER) cc_final: 0.1676 (mttp) REVERT: G 138 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.6520 (tt0) REVERT: J 7 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7554 (mttp) REVERT: K 112 MET cc_start: 0.6109 (mmt) cc_final: 0.5843 (mmt) REVERT: L 13 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7487 (mmtt) REVERT: L 60 ARG cc_start: 0.7722 (ptt180) cc_final: 0.7467 (ptt180) REVERT: L 96 LYS cc_start: 0.8402 (mttp) cc_final: 0.8105 (mttt) REVERT: N 97 ILE cc_start: 0.7992 (pt) cc_final: 0.7753 (mt) REVERT: P 23 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: T 56 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.4506 (tp30) REVERT: Y 27 ASN cc_start: 0.6936 (OUTLIER) cc_final: 0.6517 (p0) REVERT: Y 30 MET cc_start: 0.7182 (mmp) cc_final: 0.6903 (mmt) REVERT: Z 29 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7426 (mtt90) REVERT: 6 371 ARG cc_start: 0.4113 (OUTLIER) cc_final: 0.3883 (mmp80) REVERT: x 10 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7822 (mtm-85) REVERT: x 71 ARG cc_start: 0.7336 (ptm160) cc_final: 0.7103 (ptm160) REVERT: f 68 VAL cc_start: 0.7771 (t) cc_final: 0.7504 (t) REVERT: f 101 ARG cc_start: 0.7878 (ttp80) cc_final: 0.7415 (ttm170) REVERT: h 10 ARG cc_start: 0.8256 (mtm-85) cc_final: 0.7647 (mtt90) REVERT: h 91 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5609 (mm-30) REVERT: l 43 LYS cc_start: 0.3793 (OUTLIER) cc_final: 0.3372 (pttm) REVERT: l 69 ARG cc_start: 0.5442 (OUTLIER) cc_final: 0.3913 (ttp-110) REVERT: m 27 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7052 (ttmm) REVERT: m 58 SER cc_start: 0.7626 (t) cc_final: 0.7284 (m) REVERT: u 141 PHE cc_start: -0.1103 (OUTLIER) cc_final: -0.1648 (m-80) REVERT: w 89 PHE cc_start: 0.0213 (OUTLIER) cc_final: -0.0888 (p90) REVERT: c 25 ARG cc_start: 0.5867 (OUTLIER) cc_final: 0.5235 (ttm170) REVERT: c 52 VAL cc_start: 0.7970 (t) cc_final: 0.7665 (m) REVERT: c 62 ARG cc_start: 0.7819 (mpt-90) cc_final: 0.7498 (mtt180) REVERT: c 129 VAL cc_start: 0.8051 (t) cc_final: 0.7654 (p) REVERT: c 177 MET cc_start: 0.8284 (mtt) cc_final: 0.7880 (mtp) REVERT: c 187 ARG cc_start: 0.6735 (tpt-90) cc_final: 0.6450 (tpt-90) REVERT: d 150 GLU cc_start: 0.6951 (mp0) cc_final: 0.6608 (mp0) REVERT: d 155 LYS cc_start: 0.7748 (pttp) cc_final: 0.7542 (pttp) REVERT: e 1 MET cc_start: 0.5203 (tpp) cc_final: 0.4920 (tpp) REVERT: e 65 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5632 (pp20) REVERT: e 91 ARG cc_start: 0.5634 (OUTLIER) cc_final: 0.4234 (tpt90) REVERT: j 84 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6147 (mmm) REVERT: j 110 THR cc_start: 0.8446 (OUTLIER) cc_final: 0.8178 (p) REVERT: n 44 GLU cc_start: 0.2902 (OUTLIER) cc_final: 0.1105 (pt0) REVERT: n 73 ASP cc_start: 0.5977 (OUTLIER) cc_final: 0.5746 (p0) REVERT: o 14 ARG cc_start: 0.8289 (mtp-110) cc_final: 0.7275 (mtp180) outliers start: 229 outliers final: 176 residues processed: 647 average time/residue: 1.4782 time to fit residues: 1561.5958 Evaluate side-chains 657 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 456 time to evaluate : 5.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 160 LEU Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 298 VAL Chi-restraints excluded: chain 6 residue 342 LEU Chi-restraints excluded: chain 6 residue 371 ARG Chi-restraints excluded: chain x residue 10 ARG Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ARG Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 76 ILE Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 92 ASP Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 109 LYS Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 135 LYS Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 71 ILE Chi-restraints excluded: chain h residue 91 GLU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 6 ILE Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 27 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 57 ASP Chi-restraints excluded: chain l residue 67 ASP Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain m residue 27 LYS Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain u residue 141 PHE Chi-restraints excluded: chain w residue 8 MET Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 19 THR Chi-restraints excluded: chain w residue 30 ILE Chi-restraints excluded: chain w residue 48 MET Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 89 PHE Chi-restraints excluded: chain w residue 91 VAL Chi-restraints excluded: chain w residue 101 THR Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 178 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain c residue 25 ARG Chi-restraints excluded: chain c residue 43 ARG Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 116 LEU Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain j residue 118 ASN Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 73 ASP Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 49 ASN Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 21 ASP Chi-restraints excluded: chain q residue 72 ARG Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 53 MET Chi-restraints excluded: chain s residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 603 optimal weight: 0.3980 chunk 971 optimal weight: 10.0000 chunk 593 optimal weight: 7.9990 chunk 460 optimal weight: 6.9990 chunk 675 optimal weight: 3.9990 chunk 1019 optimal weight: 6.9990 chunk 938 optimal weight: 5.9990 chunk 811 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 626 optimal weight: 2.9990 chunk 497 optimal weight: 9.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 GLN N 3 HIS ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN ** 6 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 ASN ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 1.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.178 156636 Z= 0.415 Angle : 0.798 83.819 234093 Z= 0.401 Chirality : 0.045 0.888 29864 Planarity : 0.006 0.198 12746 Dihedral : 23.736 179.396 77727 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.07 % Favored : 92.88 % Rotamer: Outliers : 4.47 % Allowed : 32.85 % Favored : 62.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.10), residues: 5816 helix: 0.52 (0.11), residues: 1949 sheet: -0.52 (0.17), residues: 865 loop : -1.77 (0.10), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP T 80 HIS 0.265 0.003 HIS M 13 PHE 0.031 0.002 PHE w 68 TYR 0.023 0.002 TYR g 85 ARG 0.035 0.001 ARG 6 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 456 time to evaluate : 6.072 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: 3 29 ARG cc_start: 0.8121 (mmt-90) cc_final: 0.7855 (mtp85) REVERT: C 47 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7413 (mmm-85) REVERT: D 28 GLU cc_start: 0.6588 (tt0) cc_final: 0.6182 (tt0) REVERT: D 84 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7012 (mt) REVERT: D 109 VAL cc_start: 0.8270 (t) cc_final: 0.8022 (m) REVERT: D 168 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6176 (pp20) REVERT: E 114 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6510 (mtm180) REVERT: E 117 ARG cc_start: 0.8242 (mtp180) cc_final: 0.8037 (mtp180) REVERT: E 120 VAL cc_start: 0.8140 (m) cc_final: 0.7844 (p) REVERT: E 162 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7622 (ttm-80) REVERT: F 94 ARG cc_start: 0.5792 (OUTLIER) cc_final: 0.5384 (mmp-170) REVERT: F 144 LYS cc_start: 0.2673 (OUTLIER) cc_final: 0.1673 (mttp) REVERT: G 138 GLN cc_start: 0.6953 (OUTLIER) cc_final: 0.6516 (tt0) REVERT: J 7 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7554 (mttp) REVERT: K 112 MET cc_start: 0.6107 (mmt) cc_final: 0.5839 (mmt) REVERT: L 60 ARG cc_start: 0.7718 (ptt180) cc_final: 0.7462 (ptt180) REVERT: L 96 LYS cc_start: 0.8399 (mttp) cc_final: 0.8089 (mttt) REVERT: N 97 ILE cc_start: 0.7966 (pt) cc_final: 0.7747 (mt) REVERT: P 23 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: T 56 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.4502 (tp30) REVERT: Y 27 ASN cc_start: 0.6942 (OUTLIER) cc_final: 0.6528 (p0) REVERT: Y 30 MET cc_start: 0.7192 (mmp) cc_final: 0.6905 (mmt) REVERT: Z 29 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7418 (mtt90) REVERT: 6 371 ARG cc_start: 0.4110 (OUTLIER) cc_final: 0.3882 (mmp80) REVERT: x 10 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7819 (mtm-85) REVERT: x 71 ARG cc_start: 0.7333 (ptm160) cc_final: 0.7101 (ptm160) REVERT: f 67 ASN cc_start: 0.7457 (t0) cc_final: 0.7192 (t0) REVERT: f 68 VAL cc_start: 0.7627 (t) cc_final: 0.7363 (t) REVERT: f 85 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6533 (mt0) REVERT: f 101 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7411 (ttm170) REVERT: h 10 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7652 (mtt90) REVERT: h 91 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5603 (mm-30) REVERT: l 43 LYS cc_start: 0.3786 (OUTLIER) cc_final: 0.3376 (pttm) REVERT: l 69 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.3783 (ttp-170) REVERT: m 27 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.7051 (ttmm) REVERT: m 58 SER cc_start: 0.7619 (t) cc_final: 0.7282 (m) REVERT: u 141 PHE cc_start: -0.1103 (OUTLIER) cc_final: -0.1647 (m-80) REVERT: w 89 PHE cc_start: 0.0163 (OUTLIER) cc_final: -0.0917 (p90) REVERT: c 25 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5230 (ttm170) REVERT: c 52 VAL cc_start: 0.7966 (t) cc_final: 0.7662 (m) REVERT: c 62 ARG cc_start: 0.7817 (mpt-90) cc_final: 0.7501 (mtt180) REVERT: c 129 VAL cc_start: 0.8033 (t) cc_final: 0.7650 (p) REVERT: c 177 MET cc_start: 0.8274 (mtt) cc_final: 0.7878 (mtp) REVERT: c 187 ARG cc_start: 0.6730 (tpt-90) cc_final: 0.6413 (tpt-90) REVERT: d 150 GLU cc_start: 0.6945 (mp0) cc_final: 0.6602 (mp0) REVERT: d 155 LYS cc_start: 0.7749 (pttp) cc_final: 0.7539 (pttp) REVERT: e 1 MET cc_start: 0.5202 (tpp) cc_final: 0.4919 (tpp) REVERT: e 65 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.5632 (pp20) REVERT: e 91 ARG cc_start: 0.5630 (OUTLIER) cc_final: 0.4128 (tpt90) REVERT: j 84 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6123 (mmm) REVERT: j 110 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8175 (p) REVERT: k 30 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6958 (ptt180) REVERT: n 44 GLU cc_start: 0.2850 (OUTLIER) cc_final: 0.1126 (pt0) REVERT: n 73 ASP cc_start: 0.5994 (OUTLIER) cc_final: 0.5759 (p0) REVERT: o 14 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7280 (mtp180) outliers start: 217 outliers final: 178 residues processed: 637 average time/residue: 1.4713 time to fit residues: 1527.8326 Evaluate side-chains 663 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 457 time to evaluate : 5.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 3 residue 18 LYS Chi-restraints excluded: chain 4 residue 22 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 17 LYS Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 149 LYS Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 183 GLU Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 114 ARG Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 51 ASN Chi-restraints excluded: chain F residue 91 ARG Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 128 SER Chi-restraints excluded: chain F residue 144 LYS Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 2 ARG Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 74 MET Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 138 GLN Chi-restraints excluded: chain J residue 4 PHE Chi-restraints excluded: chain J residue 7 LYS Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 40 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 6 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 88 ASN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 87 LEU Chi-restraints excluded: chain U residue 16 LYS Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 69 GLU Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 36 ARG Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Z residue 15 ARG Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain Z residue 46 MET Chi-restraints excluded: chain 6 residue 14 VAL Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 46 THR Chi-restraints excluded: chain 6 residue 60 GLU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 100 VAL Chi-restraints excluded: chain 6 residue 160 LEU Chi-restraints excluded: chain 6 residue 239 ILE Chi-restraints excluded: chain 6 residue 255 PHE Chi-restraints excluded: chain 6 residue 298 VAL Chi-restraints excluded: chain 6 residue 342 LEU Chi-restraints excluded: chain 6 residue 345 GLN Chi-restraints excluded: chain 6 residue 371 ARG Chi-restraints excluded: chain x residue 10 ARG Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 53 ARG Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 76 ILE Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 92 ASP Chi-restraints excluded: chain x residue 120 THR Chi-restraints excluded: chain x residue 127 VAL Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain f residue 65 LEU Chi-restraints excluded: chain f residue 85 GLN Chi-restraints excluded: chain f residue 109 LYS Chi-restraints excluded: chain f residue 132 THR Chi-restraints excluded: chain f residue 135 LYS Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 34 LEU Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 71 ILE Chi-restraints excluded: chain h residue 91 GLU Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 17 LEU Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 27 THR Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 48 SER Chi-restraints excluded: chain l residue 57 ASP Chi-restraints excluded: chain l residue 67 ASP Chi-restraints excluded: chain l residue 69 ARG Chi-restraints excluded: chain l residue 78 ARG Chi-restraints excluded: chain m residue 27 LYS Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain r residue 65 MET Chi-restraints excluded: chain u residue 141 PHE Chi-restraints excluded: chain w residue 8 MET Chi-restraints excluded: chain w residue 13 VAL Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 19 THR Chi-restraints excluded: chain w residue 30 ILE Chi-restraints excluded: chain w residue 48 MET Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 89 PHE Chi-restraints excluded: chain w residue 91 VAL Chi-restraints excluded: chain w residue 101 THR Chi-restraints excluded: chain w residue 135 MET Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 178 LEU Chi-restraints excluded: chain w residue 182 VAL Chi-restraints excluded: chain w residue 185 ILE Chi-restraints excluded: chain c residue 25 ARG Chi-restraints excluded: chain c residue 43 ARG Chi-restraints excluded: chain c residue 63 ILE Chi-restraints excluded: chain c residue 90 LEU Chi-restraints excluded: chain c residue 116 LEU Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain d residue 55 VAL Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 7 VAL Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 65 GLU Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 84 VAL Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain g residue 33 VAL Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 94 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 84 MET Chi-restraints excluded: chain j residue 110 THR Chi-restraints excluded: chain j residue 118 ASN Chi-restraints excluded: chain k residue 30 ARG Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 69 GLU Chi-restraints excluded: chain k residue 78 VAL Chi-restraints excluded: chain k residue 92 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 73 ASP Chi-restraints excluded: chain n residue 81 ILE Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 67 ILE Chi-restraints excluded: chain p residue 49 ASN Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 72 ARG Chi-restraints excluded: chain s residue 29 THR Chi-restraints excluded: chain s residue 38 ILE Chi-restraints excluded: chain s residue 53 MET Chi-restraints excluded: chain s residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 644 optimal weight: 0.0070 chunk 864 optimal weight: 0.7980 chunk 248 optimal weight: 90.0000 chunk 748 optimal weight: 5.9990 chunk 119 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 812 optimal weight: 0.5980 chunk 340 optimal weight: 50.0000 chunk 834 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 HIS ** P 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN ** 6 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.153763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123012 restraints weight = 198699.262| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.19 r_work: 0.3190 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 1.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.178 156636 Z= 0.415 Angle : 0.798 83.819 234093 Z= 0.401 Chirality : 0.045 0.888 29864 Planarity : 0.006 0.198 12746 Dihedral : 23.736 179.396 77727 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.07 % Favored : 92.88 % Rotamer: Outliers : 4.26 % Allowed : 33.05 % Favored : 62.69 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.10), residues: 5816 helix: 0.52 (0.11), residues: 1949 sheet: -0.52 (0.17), residues: 865 loop : -1.77 (0.10), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP T 80 HIS 0.265 0.003 HIS M 13 PHE 0.031 0.002 PHE w 68 TYR 0.023 0.002 TYR g 85 ARG 0.035 0.001 ARG 6 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27488.61 seconds wall clock time: 486 minutes 36.80 seconds (29196.80 seconds total)