Starting phenix.real_space_refine on Sun Mar 24 21:08:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axk_15700/03_2024/8axk_15700.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axk_15700/03_2024/8axk_15700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axk_15700/03_2024/8axk_15700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axk_15700/03_2024/8axk_15700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axk_15700/03_2024/8axk_15700.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8axk_15700/03_2024/8axk_15700.pdb" } resolution = 4.05 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 4 Type Number sf(0) Gaussians S 101 5.16 5 C 28443 2.51 5 N 7082 2.21 5 O 8515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "K PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 176": "NH1" <-> "NH2" Residue "K PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "O PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 49": "OE1" <-> "OE2" Residue "X ARG 138": "NH1" <-> "NH2" Residue "X TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 138": "NH1" <-> "NH2" Residue "Z ARG 138": "NH1" <-> "NH2" Residue "0 ARG 138": "NH1" <-> "NH2" Residue "0 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 138": "NH1" <-> "NH2" Residue "4 ASP 131": "OD1" <-> "OD2" Residue "4 ARG 138": "NH1" <-> "NH2" Residue "6 ARG 138": "NH1" <-> "NH2" Residue "8 ARG 138": "NH1" <-> "NH2" Residue "8 PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ARG 138": "NH1" <-> "NH2" Residue "y ARG 138": "NH1" <-> "NH2" Residue "z TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 138": "NH1" <-> "NH2" Residue "1 ARG 138": "NH1" <-> "NH2" Residue "1 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 138": "NH1" <-> "NH2" Residue "5 ARG 138": "NH1" <-> "NH2" Residue "7 ARG 138": "NH1" <-> "NH2" Residue "9 ARG 138": "NH1" <-> "NH2" Residue "9 TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 83": "NH1" <-> "NH2" Residue "g ARG 83": "NH1" <-> "NH2" Residue "h PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 83": "NH1" <-> "NH2" Residue "p ARG 83": "NH1" <-> "NH2" Residue "q PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 83": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "v PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e0 ARG 105": "NH1" <-> "NH2" Residue "g0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g0 ARG 105": "NH1" <-> "NH2" Residue "h0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i0 ARG 105": "NH1" <-> "NH2" Residue "k0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o0 ARG 100": "NH1" <-> "NH2" Residue "p0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u0 ARG 105": "NH1" <-> "NH2" Residue "v0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v0 ARG 105": "NH1" <-> "NH2" Residue "w0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x0 PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x0 ARG 105": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44141 Number of models: 1 Model: "" Number of chains: 85 Chain: "A" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1486 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 2 Chain: "B" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1459 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain breaks: 2 Chain: "C" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1480 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 7, 'TRANS': 180} Chain breaks: 2 Chain: "D" Number of atoms: 1438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1438 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 7, 'TRANS': 175} Chain breaks: 2 Chain: "E" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1464 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain breaks: 2 Chain: "F" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2018 Classifications: {'peptide': 256} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 246} Chain: "G" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 656 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "H" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain breaks: 1 Chain: "I" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 494 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain breaks: 1 Chain: "J" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 521 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain breaks: 1 Chain: "K" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 953 Classifications: {'peptide': 113} Link IDs: {'TRANS': 112} Chain breaks: 1 Chain: "M" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 308 Classifications: {'peptide': 42} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "N" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 644 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "O" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 727 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "P" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 707 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 641 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "R" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 643 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 1 Chain: "S" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "T" 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': 2, 'TRANS': 56} Chain: "U" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "V" 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': 2, 'TRANS': 56} Chain: "W" 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': 2, 'TRANS': 56} Chain: "X" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Y" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "Z" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "0" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "2" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "4" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "6" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "8" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "x" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "y" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "z" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "1" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "3" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "5" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "7" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "9" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 497 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 3, 'TRANS': 58} Chain: "a" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "b" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "c" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "d" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "e" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "f" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "g" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "h" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "i" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "j" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "k" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 594 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "l" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "m" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "n" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "o" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "r" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "s" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "t" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 617 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 75} Chain: "u" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 638 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "v" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "w" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "a0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "b0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "c0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "d0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "e0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "f0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "g0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "h0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "i0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "j0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "k0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "l0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "m0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "n0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "o0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "p0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "q0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "r0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "s0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "t0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "u0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "v0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "w0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Chain: "x0" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 131 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 2, 'TRANS': 14} Time building chain proxies: 22.93, per 1000 atoms: 0.52 Number of scatterers: 44141 At special positions: 0 Unit cell: (148.055, 148.055, 271.203, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 101 16.00 O 8515 8.00 N 7082 7.00 C 28443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 158 " - pdb=" SG CYS F 164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.55 Conformation dependent library (CDL) restraints added in 7.7 seconds 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10836 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 16 sheets defined 76.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.78 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 16 through 25 removed outlier: 3.580A pdb=" N THR A 25 " --> pdb=" O VAL A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 41 Processing helix chain 'A' and resid 48 through 64 removed outlier: 3.513A pdb=" N LEU A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 134 through 176 Proline residue: A 140 - end of helix removed outlier: 3.687A pdb=" N LEU A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Proline residue: A 160 - end of helix Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.848A pdb=" N VAL A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 16 through 25 removed outlier: 3.543A pdb=" N THR B 25 " --> pdb=" O VAL B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 42 removed outlier: 3.579A pdb=" N GLY B 42 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 73 removed outlier: 3.788A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Proline residue: B 66 - end of helix Processing helix chain 'B' and resid 95 through 106 Processing helix chain 'B' and resid 108 through 118 removed outlier: 3.649A pdb=" N ALA B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 176 Proline residue: B 140 - end of helix removed outlier: 3.682A pdb=" N LEU B 159 " --> pdb=" O PHE B 155 " (cutoff:3.500A) Proline residue: B 160 - end of helix Processing helix chain 'B' and resid 181 through 184 Processing helix chain 'B' and resid 185 through 197 removed outlier: 4.141A pdb=" N ILE B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 16 through 24 removed outlier: 3.519A pdb=" N GLY C 24 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 41 removed outlier: 3.636A pdb=" N PHE C 30 " --> pdb=" O CYS C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 72 removed outlier: 3.640A pdb=" N LEU C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) Proline residue: C 66 - end of helix removed outlier: 3.541A pdb=" N TYR C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 106 Processing helix chain 'C' and resid 108 through 121 removed outlier: 3.560A pdb=" N ALA C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 176 Proline residue: C 140 - end of helix removed outlier: 3.739A pdb=" N LEU C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Proline residue: C 160 - end of helix Processing helix chain 'C' and resid 181 through 197 removed outlier: 4.196A pdb=" N ILE C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Proline residue: C 188 - end of helix Processing helix chain 'C' and resid 199 through 211 Processing helix chain 'D' and resid 5 through 16 Processing helix chain 'D' and resid 16 through 25 Processing helix chain 'D' and resid 26 through 41 Processing helix chain 'D' and resid 48 through 64 removed outlier: 3.518A pdb=" N LEU D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 71 removed outlier: 3.712A pdb=" N GLY D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 134 through 176 Proline residue: D 140 - end of helix removed outlier: 3.640A pdb=" N LEU D 159 " --> pdb=" O PHE D 155 " (cutoff:3.500A) Proline residue: D 160 - end of helix Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.547A pdb=" N VAL D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix Processing helix chain 'D' and resid 199 through 212 Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 16 through 24 Processing helix chain 'E' and resid 26 through 41 Processing helix chain 'E' and resid 48 through 72 Proline residue: E 66 - end of helix Processing helix chain 'E' and resid 94 through 106 Processing helix chain 'E' and resid 108 through 120 removed outlier: 3.887A pdb=" N ALA E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 176 Proline residue: E 140 - end of helix removed outlier: 3.975A pdb=" N LEU E 159 " --> pdb=" O PHE E 155 " (cutoff:3.500A) Proline residue: E 160 - end of helix Processing helix chain 'E' and resid 181 through 197 removed outlier: 4.136A pdb=" N ILE E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 187 " --> pdb=" O ILE E 183 " (cutoff:3.500A) Proline residue: E 188 - end of helix Processing helix chain 'E' and resid 198 through 212 removed outlier: 3.631A pdb=" N ILE E 202 " --> pdb=" O ASP E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 30 Proline residue: F 26 - end of helix Processing helix chain 'F' and resid 40 through 58 removed outlier: 3.877A pdb=" N ILE F 45 " --> pdb=" O PRO F 41 " (cutoff:3.500A) Proline residue: F 46 - end of helix Processing helix chain 'F' and resid 70 through 90 removed outlier: 4.074A pdb=" N LEU F 74 " --> pdb=" O HIS F 70 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 108 Processing helix chain 'F' and resid 110 through 116 Processing helix chain 'F' and resid 125 through 141 Processing helix chain 'F' and resid 142 through 158 Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 173 through 207 Proline residue: F 188 - end of helix Processing helix chain 'F' and resid 212 through 231 Processing helix chain 'F' and resid 235 through 252 removed outlier: 3.947A pdb=" N LYS F 239 " --> pdb=" O ILE F 235 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL F 240 " --> pdb=" O TYR F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 41 removed outlier: 4.468A pdb=" N TRP G 21 " --> pdb=" O ILE G 17 " (cutoff:3.500A) Proline residue: G 22 - end of helix Processing helix chain 'G' and resid 45 through 63 removed outlier: 3.733A pdb=" N PHE G 49 " --> pdb=" O GLN G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 84 removed outlier: 3.655A pdb=" N SER G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 35 removed outlier: 3.883A pdb=" N TRP H 21 " --> pdb=" O ILE H 17 " (cutoff:3.500A) Proline residue: H 22 - end of helix Processing helix chain 'H' and resid 48 through 85 removed outlier: 5.269A pdb=" N GLY H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N TRP H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER H 84 " --> pdb=" O PHE H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 25 removed outlier: 3.636A pdb=" N TRP I 21 " --> pdb=" O ILE I 17 " (cutoff:3.500A) Proline residue: I 22 - end of helix Processing helix chain 'I' and resid 49 through 85 removed outlier: 5.399A pdb=" N GLY I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N TRP I 66 " --> pdb=" O LEU I 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 27 removed outlier: 3.810A pdb=" N TRP J 21 " --> pdb=" O ILE J 17 " (cutoff:3.500A) Proline residue: J 22 - end of helix Processing helix chain 'J' and resid 49 through 85 removed outlier: 4.513A pdb=" N GLY J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TRP J 66 " --> pdb=" O LEU J 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 41 removed outlier: 3.816A pdb=" N PHE K 39 " --> pdb=" O LEU K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 63 Processing helix chain 'K' and resid 68 through 83 Processing helix chain 'K' and resid 132 through 155 removed outlier: 3.976A pdb=" N LYS K 136 " --> pdb=" O LYS K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 156 through 163 Processing helix chain 'K' and resid 169 through 186 removed outlier: 4.131A pdb=" N LEU K 186 " --> pdb=" O ILE K 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 95 Processing helix chain 'N' and resid 25 through 54 Processing helix chain 'N' and resid 55 through 58 removed outlier: 3.579A pdb=" N LEU N 58 " --> pdb=" O PRO N 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 55 through 58' Processing helix chain 'N' and resid 59 through 97 removed outlier: 3.890A pdb=" N SER N 97 " --> pdb=" O THR N 93 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 54 Processing helix chain 'O' and resid 59 through 96 Processing helix chain 'P' and resid 25 through 54 Processing helix chain 'P' and resid 55 through 58 removed outlier: 3.667A pdb=" N LEU P 58 " --> pdb=" O PRO P 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 55 through 58' Processing helix chain 'P' and resid 59 through 96 Processing helix chain 'Q' and resid 26 through 54 Processing helix chain 'Q' and resid 59 through 97 removed outlier: 4.144A pdb=" N SER Q 97 " --> pdb=" O THR Q 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 54 Processing helix chain 'R' and resid 59 through 97 removed outlier: 4.243A pdb=" N SER R 97 " --> pdb=" O THR R 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 40 Processing helix chain 'S' and resid 43 through 83 removed outlier: 3.813A pdb=" N ILE S 79 " --> pdb=" O ASP S 75 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN S 81 " --> pdb=" O ALA S 77 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE S 82 " --> pdb=" O ILE S 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 40 Processing helix chain 'T' and resid 43 through 83 removed outlier: 3.612A pdb=" N ILE T 79 " --> pdb=" O ASP T 75 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE T 82 " --> pdb=" O ILE T 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 40 Processing helix chain 'U' and resid 43 through 82 removed outlier: 3.680A pdb=" N ILE U 79 " --> pdb=" O ASP U 75 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN U 81 " --> pdb=" O ALA U 77 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE U 82 " --> pdb=" O ILE U 78 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 40 Processing helix chain 'V' and resid 43 through 82 removed outlier: 3.587A pdb=" N ILE V 79 " --> pdb=" O ASP V 75 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE V 82 " --> pdb=" O ILE V 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 40 Processing helix chain 'W' and resid 43 through 83 removed outlier: 3.724A pdb=" N ILE W 79 " --> pdb=" O ASP W 75 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE W 82 " --> pdb=" O ILE W 78 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 132 Processing helix chain 'X' and resid 155 through 168 Processing helix chain 'Y' and resid 121 through 132 Processing helix chain 'Y' and resid 155 through 168 Processing helix chain 'Z' and resid 121 through 132 Processing helix chain 'Z' and resid 155 through 168 Processing helix chain '0' and resid 121 through 132 Processing helix chain '0' and resid 155 through 168 Processing helix chain '2' and resid 121 through 132 Processing helix chain '2' and resid 155 through 168 Processing helix chain '4' and resid 121 through 132 Processing helix chain '4' and resid 155 through 168 Processing helix chain '6' and resid 121 through 132 Processing helix chain '6' and resid 155 through 168 Processing helix chain '8' and resid 121 through 132 Processing helix chain '8' and resid 155 through 168 Processing helix chain 'x' and resid 121 through 132 Processing helix chain 'x' and resid 155 through 168 Processing helix chain 'y' and resid 121 through 132 Processing helix chain 'y' and resid 155 through 169 Processing helix chain 'z' and resid 121 through 132 Processing helix chain 'z' and resid 155 through 168 Processing helix chain '1' and resid 121 through 132 Processing helix chain '1' and resid 155 through 168 Processing helix chain '3' and resid 121 through 132 Processing helix chain '3' and resid 155 through 168 Processing helix chain '5' and resid 121 through 132 Processing helix chain '5' and resid 155 through 169 Processing helix chain '7' and resid 121 through 132 Processing helix chain '7' and resid 155 through 168 Processing helix chain '9' and resid 121 through 132 Processing helix chain '9' and resid 155 through 168 Processing helix chain 'a' and resid 11 through 23 removed outlier: 3.648A pdb=" N THR a 23 " --> pdb=" O PHE a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 24 through 40 Processing helix chain 'a' and resid 43 through 80 Processing helix chain 'b' and resid 11 through 23 Processing helix chain 'b' and resid 24 through 40 removed outlier: 3.530A pdb=" N GLY b 28 " --> pdb=" O GLN b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 43 through 80 removed outlier: 3.514A pdb=" N GLN b 80 " --> pdb=" O ALA b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 83 No H-bonds generated for 'chain 'b' and resid 81 through 83' Processing helix chain 'c' and resid 11 through 23 removed outlier: 3.513A pdb=" N THR c 23 " --> pdb=" O PHE c 19 " (cutoff:3.500A) Processing helix chain 'c' and resid 24 through 40 removed outlier: 3.590A pdb=" N GLY c 28 " --> pdb=" O GLN c 24 " (cutoff:3.500A) Processing helix chain 'c' and resid 43 through 81 removed outlier: 3.979A pdb=" N ASN c 81 " --> pdb=" O ALA c 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 11 through 23 Processing helix chain 'd' and resid 24 through 40 Processing helix chain 'd' and resid 43 through 80 Processing helix chain 'd' and resid 81 through 83 No H-bonds generated for 'chain 'd' and resid 81 through 83' Processing helix chain 'e' and resid 11 through 22 Processing helix chain 'e' and resid 24 through 40 Processing helix chain 'e' and resid 43 through 81 removed outlier: 3.923A pdb=" N ASN e 81 " --> pdb=" O ALA e 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 11 through 23 removed outlier: 3.525A pdb=" N THR f 23 " --> pdb=" O PHE f 19 " (cutoff:3.500A) Processing helix chain 'f' and resid 24 through 40 Processing helix chain 'f' and resid 43 through 80 Processing helix chain 'g' and resid 11 through 23 Processing helix chain 'g' and resid 24 through 40 Processing helix chain 'g' and resid 43 through 81 removed outlier: 4.013A pdb=" N ASN g 81 " --> pdb=" O ALA g 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 22 Processing helix chain 'h' and resid 24 through 40 removed outlier: 3.693A pdb=" N GLY h 28 " --> pdb=" O GLN h 24 " (cutoff:3.500A) Processing helix chain 'h' and resid 43 through 80 Processing helix chain 'h' and resid 81 through 83 No H-bonds generated for 'chain 'h' and resid 81 through 83' Processing helix chain 'i' and resid 12 through 22 Processing helix chain 'i' and resid 24 through 40 removed outlier: 3.668A pdb=" N GLY i 28 " --> pdb=" O GLN i 24 " (cutoff:3.500A) Processing helix chain 'i' and resid 43 through 81 removed outlier: 3.854A pdb=" N ASN i 81 " --> pdb=" O ALA i 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 23 removed outlier: 3.593A pdb=" N THR j 23 " --> pdb=" O PHE j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 24 through 40 removed outlier: 3.507A pdb=" N GLY j 28 " --> pdb=" O GLN j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 43 through 81 removed outlier: 3.925A pdb=" N ASN j 81 " --> pdb=" O ALA j 77 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 23 removed outlier: 3.804A pdb=" N THR k 23 " --> pdb=" O PHE k 19 " (cutoff:3.500A) Processing helix chain 'k' and resid 24 through 40 removed outlier: 3.557A pdb=" N GLY k 28 " --> pdb=" O GLN k 24 " (cutoff:3.500A) Processing helix chain 'k' and resid 43 through 80 Processing helix chain 'k' and resid 81 through 83 No H-bonds generated for 'chain 'k' and resid 81 through 83' Processing helix chain 'l' and resid 12 through 23 removed outlier: 3.547A pdb=" N THR l 23 " --> pdb=" O PHE l 19 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 40 removed outlier: 3.539A pdb=" N GLY l 28 " --> pdb=" O GLN l 24 " (cutoff:3.500A) Processing helix chain 'l' and resid 43 through 81 removed outlier: 3.573A pdb=" N ASN l 81 " --> pdb=" O ALA l 77 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 23 Processing helix chain 'm' and resid 24 through 40 Processing helix chain 'm' and resid 43 through 80 Processing helix chain 'n' and resid 11 through 23 removed outlier: 3.634A pdb=" N THR n 23 " --> pdb=" O PHE n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 24 through 40 Processing helix chain 'n' and resid 43 through 80 Processing helix chain 'o' and resid 11 through 23 Processing helix chain 'o' and resid 24 through 40 Processing helix chain 'o' and resid 43 through 80 Processing helix chain 'o' and resid 81 through 83 No H-bonds generated for 'chain 'o' and resid 81 through 83' Processing helix chain 'p' and resid 11 through 23 removed outlier: 3.611A pdb=" N THR p 23 " --> pdb=" O PHE p 19 " (cutoff:3.500A) Processing helix chain 'p' and resid 24 through 40 removed outlier: 3.538A pdb=" N GLY p 28 " --> pdb=" O GLN p 24 " (cutoff:3.500A) Processing helix chain 'p' and resid 43 through 81 removed outlier: 3.921A pdb=" N ASN p 81 " --> pdb=" O ALA p 77 " (cutoff:3.500A) Processing helix chain 'q' and resid 11 through 23 removed outlier: 3.876A pdb=" N THR q 23 " --> pdb=" O PHE q 19 " (cutoff:3.500A) Processing helix chain 'q' and resid 24 through 40 removed outlier: 3.537A pdb=" N GLY q 28 " --> pdb=" O GLN q 24 " (cutoff:3.500A) Processing helix chain 'q' and resid 43 through 80 Processing helix chain 'r' and resid 11 through 23 removed outlier: 3.764A pdb=" N THR r 23 " --> pdb=" O PHE r 19 " (cutoff:3.500A) Processing helix chain 'r' and resid 24 through 40 removed outlier: 3.686A pdb=" N GLY r 28 " --> pdb=" O GLN r 24 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 80 Processing helix chain 's' and resid 11 through 23 Processing helix chain 's' and resid 24 through 40 Processing helix chain 's' and resid 43 through 80 removed outlier: 3.567A pdb=" N GLN s 80 " --> pdb=" O ALA s 76 " (cutoff:3.500A) Processing helix chain 's' and resid 81 through 83 No H-bonds generated for 'chain 's' and resid 81 through 83' Processing helix chain 't' and resid 11 through 23 removed outlier: 3.542A pdb=" N THR t 23 " --> pdb=" O PHE t 19 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 40 Processing helix chain 't' and resid 43 through 80 Processing helix chain 'u' and resid 11 through 23 removed outlier: 3.614A pdb=" N THR u 23 " --> pdb=" O PHE u 19 " (cutoff:3.500A) Processing helix chain 'u' and resid 24 through 40 removed outlier: 3.918A pdb=" N GLY u 28 " --> pdb=" O GLN u 24 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 80 Processing helix chain 'u' and resid 81 through 83 No H-bonds generated for 'chain 'u' and resid 81 through 83' Processing helix chain 'v' and resid 11 through 23 removed outlier: 3.986A pdb=" N THR v 23 " --> pdb=" O PHE v 19 " (cutoff:3.500A) Processing helix chain 'v' and resid 24 through 40 removed outlier: 3.644A pdb=" N GLY v 28 " --> pdb=" O GLN v 24 " (cutoff:3.500A) Processing helix chain 'v' and resid 43 through 81 removed outlier: 3.517A pdb=" N GLN v 80 " --> pdb=" O ALA v 76 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN v 81 " --> pdb=" O ALA v 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 23 removed outlier: 3.542A pdb=" N THR w 23 " --> pdb=" O PHE w 19 " (cutoff:3.500A) Processing helix chain 'w' and resid 24 through 40 removed outlier: 3.618A pdb=" N GLY w 28 " --> pdb=" O GLN w 24 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN w 40 " --> pdb=" O LYS w 36 " (cutoff:3.500A) Processing helix chain 'w' and resid 43 through 81 removed outlier: 3.518A pdb=" N GLN w 80 " --> pdb=" O ALA w 76 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASN w 81 " --> pdb=" O ALA w 77 " (cutoff:3.500A) Processing helix chain 'a0' and resid 98 through 106 Processing helix chain 'b0' and resid 98 through 106 Processing helix chain 'c0' and resid 98 through 106 Processing helix chain 'd0' and resid 98 through 106 Processing helix chain 'e0' and resid 98 through 106 Processing helix chain 'f0' and resid 98 through 106 Processing helix chain 'g0' and resid 98 through 106 Processing helix chain 'h0' and resid 98 through 106 Processing helix chain 'i0' and resid 98 through 106 Processing helix chain 'j0' and resid 98 through 106 removed outlier: 3.520A pdb=" N GLUj0 102 " --> pdb=" O SERj0 98 " (cutoff:3.500A) Processing helix chain 'k0' and resid 98 through 106 Processing helix chain 'l0' and resid 98 through 106 Processing helix chain 'm0' and resid 98 through 106 Processing helix chain 'n0' and resid 98 through 106 Processing helix chain 'o0' and resid 98 through 106 Processing helix chain 'p0' and resid 98 through 106 Processing helix chain 'q0' and resid 98 through 106 Processing helix chain 'r0' and resid 98 through 106 Processing helix chain 's0' and resid 98 through 106 Processing helix chain 't0' and resid 98 through 106 removed outlier: 4.070A pdb=" N GLUt0 102 " --> pdb=" O SERt0 98 " (cutoff:3.500A) Processing helix chain 'u0' and resid 98 through 106 Processing helix chain 'v0' and resid 98 through 106 Processing helix chain 'w0' and resid 98 through 106 Processing helix chain 'x0' and resid 98 through 106 Processing sheet with id=AA1, first strand: chain 'N' and resid 11 through 14 Processing sheet with id=AA2, first strand: chain 'O' and resid 11 through 14 Processing sheet with id=AA3, first strand: chain 'P' and resid 11 through 14 Processing sheet with id=AA4, first strand: chain 'Q' and resid 11 through 14 Processing sheet with id=AA5, first strand: chain 'R' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'X' and resid 111 through 116 Processing sheet with id=AA7, first strand: chain 'Z' and resid 111 through 116 Processing sheet with id=AA8, first strand: chain '2' and resid 111 through 116 Processing sheet with id=AA9, first strand: chain '4' and resid 111 through 116 Processing sheet with id=AB1, first strand: chain '8' and resid 111 through 116 Processing sheet with id=AB2, first strand: chain 'x' and resid 111 through 116 Processing sheet with id=AB3, first strand: chain 'y' and resid 111 through 116 Processing sheet with id=AB4, first strand: chain 'z' and resid 111 through 116 Processing sheet with id=AB5, first strand: chain '1' and resid 111 through 116 Processing sheet with id=AB6, first strand: chain '5' and resid 111 through 116 Processing sheet with id=AB7, first strand: chain '7' and resid 111 through 116 3327 hydrogen bonds defined for protein. 9915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.64 Time building geometry restraints manager: 19.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13971 1.34 - 1.46: 9401 1.46 - 1.58: 21297 1.58 - 1.69: 0 1.69 - 1.81: 189 Bond restraints: 44858 Sorted by residual: bond pdb=" C VAL B 46 " pdb=" N PRO B 47 " ideal model delta sigma weight residual 1.337 1.350 -0.013 9.80e-03 1.04e+04 1.86e+00 bond pdb=" N VALe0 96 " pdb=" CA VALe0 96 " ideal model delta sigma weight residual 1.459 1.473 -0.014 1.25e-02 6.40e+03 1.31e+00 bond pdb=" CB ILE C 153 " pdb=" CG2 ILE C 153 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.12e+00 bond pdb=" CA ILE K 33 " pdb=" CB ILE K 33 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.02e+00 bond pdb=" CA ILE K 131 " pdb=" C ILE K 131 " ideal model delta sigma weight residual 1.523 1.535 -0.012 1.27e-02 6.20e+03 9.65e-01 ... (remaining 44853 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.21: 1015 106.21 - 113.15: 25390 113.15 - 120.09: 15189 120.09 - 127.03: 18992 127.03 - 133.97: 304 Bond angle restraints: 60890 Sorted by residual: angle pdb=" C ILE O 4 " pdb=" N TYR O 5 " pdb=" CA TYR O 5 " ideal model delta sigma weight residual 120.09 125.08 -4.99 1.25e+00 6.40e-01 1.59e+01 angle pdb=" N VAL K 31 " pdb=" CA VAL K 31 " pdb=" C VAL K 31 " ideal model delta sigma weight residual 111.77 108.27 3.50 1.04e+00 9.25e-01 1.13e+01 angle pdb=" C SER T 42 " pdb=" N ASN T 43 " pdb=" CA ASN T 43 " ideal model delta sigma weight residual 121.61 117.19 4.42 1.39e+00 5.18e-01 1.01e+01 angle pdb=" N SERp0 94 " pdb=" CA SERp0 94 " pdb=" C SERp0 94 " ideal model delta sigma weight residual 108.19 112.16 -3.97 1.29e+00 6.01e-01 9.49e+00 angle pdb=" C PHE p 82 " pdb=" N ARG p 83 " pdb=" CA ARG p 83 " ideal model delta sigma weight residual 121.70 126.85 -5.15 1.80e+00 3.09e-01 8.19e+00 ... (remaining 60885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 26017 17.42 - 34.85: 1043 34.85 - 52.27: 240 52.27 - 69.70: 45 69.70 - 87.12: 16 Dihedral angle restraints: 27361 sinusoidal: 10773 harmonic: 16588 Sorted by residual: dihedral pdb=" CA ILE R 12 " pdb=" C ILE R 12 " pdb=" N ILE R 13 " pdb=" CA ILE R 13 " ideal model delta harmonic sigma weight residual 180.00 -155.91 -24.09 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA PRO F 32 " pdb=" C PRO F 32 " pdb=" N PHE F 33 " pdb=" CA PHE F 33 " ideal model delta harmonic sigma weight residual 180.00 155.98 24.02 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL E 46 " pdb=" C VAL E 46 " pdb=" N PRO E 47 " pdb=" CA PRO E 47 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.88e+01 ... (remaining 27358 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 5610 0.037 - 0.073: 1324 0.073 - 0.110: 355 0.110 - 0.146: 77 0.146 - 0.183: 3 Chirality restraints: 7369 Sorted by residual: chirality pdb=" CB ILE K 131 " pdb=" CA ILE K 131 " pdb=" CG1 ILE K 131 " pdb=" CG2 ILE K 131 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.33e-01 chirality pdb=" CA PROt0 99 " pdb=" N PROt0 99 " pdb=" C PROt0 99 " pdb=" CB PROt0 99 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA ILE y 120 " pdb=" N ILE y 120 " pdb=" C ILE y 120 " pdb=" CB ILE y 120 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 ... (remaining 7366 not shown) Planarity restraints: 7620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 10 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" C VAL P 10 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL P 10 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP P 11 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHEo0 90 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PROo0 91 " -0.100 5.00e-02 4.00e+02 pdb=" CA PROo0 91 " 0.030 5.00e-02 4.00e+02 pdb=" CD PROo0 91 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL c 5 " 0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO c 6 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO c 6 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO c 6 " 0.028 5.00e-02 4.00e+02 ... (remaining 7617 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1062 2.71 - 3.26: 45875 3.26 - 3.81: 72735 3.81 - 4.35: 79862 4.35 - 4.90: 145541 Nonbonded interactions: 345075 Sorted by model distance: nonbonded pdb=" O ALA W 38 " pdb=" OG1 THR h 23 " model vdw 2.167 2.440 nonbonded pdb=" O ALA V 38 " pdb=" OG1 THR i 23 " model vdw 2.181 2.440 nonbonded pdb=" O VAL D 21 " pdb=" OG1 THR D 25 " model vdw 2.185 2.440 nonbonded pdb=" NZ LYS Q 14 " pdb=" OD1 ASN X 164 " model vdw 2.193 2.520 nonbonded pdb=" O THR Z 149 " pdb=" OH TYR z 128 " model vdw 2.194 2.440 ... (remaining 345070 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = (chain 'A' and (resid 1 through 71 or resid 94 through 214)) selection = (chain 'B' and (resid 1 through 71 or resid 94 through 120 or resid 131 through \ 214)) selection = (chain 'C' and (resid 1 through 71 or resid 94 through 120 or resid 131 through \ 214)) selection = (chain 'D' and (resid 1 through 120 or resid 131 through 214)) selection = (chain 'E' and (resid 1 through 71 or resid 94 through 130 or resid 132 through \ 214)) } ncs_group { reference = (chain 'G' and (resid 1 through 36 or resid 47 through 85)) selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and (resid 1 through 25 or resid 48 through 85)) } ncs_group { reference = (chain 'N' and (resid 8 through 14 or resid 24 through 97)) selection = (chain 'O' and (resid 8 through 14 or resid 24 through 97)) selection = (chain 'P' and (resid 8 through 14 or resid 24 through 97)) selection = (chain 'Q' and (resid 8 through 14 or resid 16 through 97)) selection = (chain 'R' and (resid 8 through 14 or resid 16 or resid 25 through 97)) } ncs_group { reference = (chain 'S' and resid 25 through 83) selection = chain 'T' selection = (chain 'U' and resid 25 through 83) selection = chain 'V' selection = chain 'W' } ncs_group { reference = (chain 'a' and resid 9 through 83) selection = (chain 'b' and resid 9 through 83) selection = (chain 'c' and resid 9 through 83) selection = (chain 'd' and resid 9 through 83) selection = (chain 'e' and resid 9 through 83) selection = (chain 'f' and resid 9 through 83) selection = (chain 'g' and resid 9 through 83) selection = chain 'h' selection = chain 'i' selection = (chain 'j' and resid 9 through 83) selection = chain 'k' selection = (chain 'l' and resid 9 through 83) selection = (chain 'm' and resid 9 through 83) selection = (chain 'n' and resid 9 through 83) selection = (chain 'o' and resid 9 through 83) selection = (chain 'p' and resid 9 through 83) selection = (chain 'q' and resid 9 through 83) selection = (chain 'r' and resid 9 through 83) selection = (chain 's' and resid 9 through 83) selection = (chain 't' and resid 9 through 83) selection = (chain 'u' and resid 9 through 83) selection = (chain 'v' and resid 9 through 83) selection = (chain 'w' and resid 9 through 83) } ncs_group { reference = chain 'a0' selection = chain 'b0' selection = chain 'c0' selection = chain 'd0' selection = chain 'e0' selection = chain 'f0' selection = chain 'g0' selection = chain 'h0' selection = chain 'i0' selection = chain 'j0' selection = chain 'k0' selection = chain 'l0' selection = chain 'm0' selection = chain 'n0' selection = chain 'o0' selection = chain 'p0' selection = chain 'q0' selection = chain 'r0' selection = chain 's0' selection = chain 't0' selection = chain 'u0' selection = chain 'v0' selection = chain 'w0' selection = chain 'x0' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 24.620 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 111.100 Find NCS groups from input model: 3.670 Set up NCS constraints: 0.780 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.002 0.038 44858 Z= 0.149 Angle : 0.465 6.197 60890 Z= 0.262 Chirality : 0.036 0.183 7369 Planarity : 0.004 0.058 7620 Dihedral : 10.517 87.125 16522 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.27 % Allowed : 5.51 % Favored : 91.22 % 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: 3.62 (0.12), residues: 5404 helix: 3.57 (0.08), residues: 4144 sheet: 1.63 (0.33), residues: 192 loop : -2.78 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 174 HIS 0.002 0.000 HIS F 11 PHE 0.018 0.001 PHE K 45 TYR 0.012 0.001 TYR 1 151 ARG 0.003 0.000 ARG o 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2737 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 2573 time to evaluate : 5.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8942 (mmm) cc_final: 0.8657 (mmm) REVERT: A 68 ILE cc_start: 0.9483 (mt) cc_final: 0.9151 (mt) REVERT: A 69 GLU cc_start: 0.7988 (tp30) cc_final: 0.7078 (mm-30) REVERT: A 96 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8955 (tt) REVERT: A 97 MET cc_start: 0.8332 (tpt) cc_final: 0.8066 (tpt) REVERT: A 98 GLU cc_start: 0.8594 (tp30) cc_final: 0.8360 (tp30) REVERT: A 101 GLN cc_start: 0.8887 (tt0) cc_final: 0.8391 (tm-30) REVERT: A 142 TYR cc_start: 0.9304 (t80) cc_final: 0.8819 (t80) REVERT: A 152 LYS cc_start: 0.9382 (tttt) cc_final: 0.9169 (ttpp) REVERT: A 179 MET cc_start: 0.8279 (mmm) cc_final: 0.7966 (mmm) REVERT: A 205 LYS cc_start: 0.9077 (mttt) cc_final: 0.8295 (tttt) REVERT: A 208 ILE cc_start: 0.8101 (mm) cc_final: 0.7808 (mm) REVERT: B 44 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8565 (mm-40) REVERT: B 65 LYS cc_start: 0.8856 (tttp) cc_final: 0.8362 (tttt) REVERT: B 67 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8264 (tp) REVERT: B 69 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7772 (mm-30) REVERT: B 96 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8361 (tt) REVERT: B 120 GLU cc_start: 0.6180 (mt-10) cc_final: 0.5884 (mp0) REVERT: B 133 TYR cc_start: 0.7513 (m-10) cc_final: 0.6847 (m-10) REVERT: B 190 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8621 (mtmm) REVERT: B 211 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7318 (t80) REVERT: C 117 ARG cc_start: 0.8447 (mtt180) cc_final: 0.8236 (tpt170) REVERT: C 146 GLU cc_start: 0.8544 (tp30) cc_final: 0.8003 (mm-30) REVERT: C 164 VAL cc_start: 0.9572 (t) cc_final: 0.9338 (t) REVERT: C 165 ASP cc_start: 0.7841 (m-30) cc_final: 0.7471 (m-30) REVERT: C 167 VAL cc_start: 0.9265 (t) cc_final: 0.9047 (p) REVERT: C 193 LEU cc_start: 0.9443 (tp) cc_final: 0.9215 (tt) REVERT: D 2 LEU cc_start: 0.9142 (mt) cc_final: 0.8740 (mt) REVERT: D 6 SER cc_start: 0.8595 (m) cc_final: 0.7908 (p) REVERT: D 27 TYR cc_start: 0.9078 (t80) cc_final: 0.8778 (t80) REVERT: D 44 GLN cc_start: 0.8300 (pm20) cc_final: 0.7847 (pm20) REVERT: D 158 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8497 (m-80) REVERT: D 170 SER cc_start: 0.8883 (m) cc_final: 0.8635 (t) REVERT: E 36 MET cc_start: 0.8695 (mmm) cc_final: 0.7871 (mmm) REVERT: E 64 MET cc_start: 0.8617 (mmm) cc_final: 0.7565 (mmm) REVERT: E 100 LYS cc_start: 0.9256 (mtpm) cc_final: 0.9021 (mtpp) REVERT: E 158 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8182 (m-80) REVERT: E 184 THR cc_start: 0.9250 (p) cc_final: 0.8494 (t) REVERT: F 69 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7169 (pm20) REVERT: F 128 LYS cc_start: 0.8818 (tptt) cc_final: 0.8538 (ttpt) REVERT: F 140 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6737 (t80) REVERT: F 145 VAL cc_start: 0.8664 (t) cc_final: 0.7796 (t) REVERT: F 152 GLN cc_start: 0.9178 (tt0) cc_final: 0.8578 (tp40) REVERT: F 170 ASN cc_start: 0.8365 (m-40) cc_final: 0.8140 (m-40) REVERT: G 7 MET cc_start: 0.8617 (mmm) cc_final: 0.8336 (tpp) REVERT: G 57 SER cc_start: 0.9206 (t) cc_final: 0.8862 (p) REVERT: G 74 PHE cc_start: 0.9203 (t80) cc_final: 0.8772 (t80) REVERT: G 75 CYS cc_start: 0.8613 (m) cc_final: 0.8334 (m) REVERT: H 6 TYR cc_start: 0.7253 (t80) cc_final: 0.7030 (t80) REVERT: H 58 ILE cc_start: 0.8498 (mm) cc_final: 0.8281 (mm) REVERT: H 59 SER cc_start: 0.8706 (m) cc_final: 0.8495 (m) REVERT: H 80 PHE cc_start: 0.6645 (OUTLIER) cc_final: 0.6099 (m-80) REVERT: H 81 LEU cc_start: 0.8738 (mt) cc_final: 0.8337 (mt) REVERT: H 83 LYS cc_start: 0.8699 (tptt) cc_final: 0.8495 (tppp) REVERT: I 1 MET cc_start: 0.7473 (ptm) cc_final: 0.7230 (ptp) REVERT: I 5 VAL cc_start: 0.9240 (t) cc_final: 0.8677 (p) REVERT: I 9 ASN cc_start: 0.8422 (m-40) cc_final: 0.8174 (m-40) REVERT: I 18 PHE cc_start: 0.8925 (m-10) cc_final: 0.8513 (m-10) REVERT: I 49 PHE cc_start: 0.6881 (OUTLIER) cc_final: 0.6274 (m-10) REVERT: I 53 LEU cc_start: 0.8093 (tp) cc_final: 0.7707 (tp) REVERT: I 60 LEU cc_start: 0.8698 (mt) cc_final: 0.8408 (mt) REVERT: I 82 ILE cc_start: 0.8984 (mt) cc_final: 0.8550 (mt) REVERT: J 3 ASP cc_start: 0.7523 (p0) cc_final: 0.7307 (p0) REVERT: J 66 TRP cc_start: 0.9161 (t60) cc_final: 0.8695 (t-100) REVERT: J 77 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7762 (mt-10) REVERT: K 46 SER cc_start: 0.7643 (m) cc_final: 0.6954 (t) REVERT: K 51 MET cc_start: 0.7789 (mmt) cc_final: 0.6948 (mmt) REVERT: K 132 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.6748 (mttt) REVERT: K 139 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.6819 (mm) REVERT: K 156 ARG cc_start: 0.6778 (ttp-110) cc_final: 0.6273 (ptm-80) REVERT: K 157 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7732 (pttp) REVERT: K 177 LEU cc_start: 0.9155 (tp) cc_final: 0.8871 (tp) REVERT: K 182 ILE cc_start: 0.8092 (tp) cc_final: 0.7862 (tp) REVERT: M 72 ASN cc_start: 0.8199 (m-40) cc_final: 0.7988 (t0) REVERT: N 14 LYS cc_start: 0.3229 (OUTLIER) cc_final: 0.2923 (mtmt) REVERT: N 46 SER cc_start: 0.8847 (m) cc_final: 0.8523 (p) REVERT: N 58 LEU cc_start: 0.9276 (mt) cc_final: 0.8980 (mt) REVERT: P 10 VAL cc_start: 0.6838 (OUTLIER) cc_final: 0.6311 (m) REVERT: P 12 ILE cc_start: 0.8514 (mt) cc_final: 0.8050 (mt) REVERT: P 57 SER cc_start: 0.9326 (m) cc_final: 0.8699 (p) REVERT: Q 13 ILE cc_start: 0.7868 (OUTLIER) cc_final: 0.7458 (mt) REVERT: Q 49 MET cc_start: 0.9056 (mmt) cc_final: 0.8741 (mmm) REVERT: R 47 GLN cc_start: 0.8606 (tp40) cc_final: 0.8195 (tm-30) REVERT: R 51 MET cc_start: 0.8125 (ttm) cc_final: 0.7855 (ttp) REVERT: S 36 LYS cc_start: 0.9164 (mtmt) cc_final: 0.8963 (mtpt) REVERT: S 69 LYS cc_start: 0.9048 (tttp) cc_final: 0.8285 (tptm) REVERT: U 61 ARG cc_start: 0.8990 (mmt180) cc_final: 0.8497 (tpp-160) REVERT: V 32 LEU cc_start: 0.8735 (mt) cc_final: 0.8271 (tt) REVERT: V 50 TYR cc_start: 0.9196 (t80) cc_final: 0.8885 (t80) REVERT: V 59 LEU cc_start: 0.9087 (mt) cc_final: 0.8830 (mt) REVERT: V 64 GLN cc_start: 0.8626 (tt0) cc_final: 0.8373 (tt0) REVERT: W 39 LYS cc_start: 0.8420 (mttt) cc_final: 0.7837 (mptt) REVERT: W 40 ASN cc_start: 0.8781 (t0) cc_final: 0.8114 (t0) REVERT: W 43 ASN cc_start: 0.8640 (t0) cc_final: 0.8040 (t0) REVERT: X 142 ARG cc_start: 0.8241 (mmt-90) cc_final: 0.7845 (mmt-90) REVERT: Y 112 SER cc_start: 0.7747 (p) cc_final: 0.7308 (m) REVERT: Y 123 ASN cc_start: 0.8639 (t0) cc_final: 0.8380 (t0) REVERT: Y 131 ASP cc_start: 0.7193 (t70) cc_final: 0.6736 (t70) REVERT: Z 111 ILE cc_start: 0.9198 (mt) cc_final: 0.8899 (pt) REVERT: Z 112 SER cc_start: 0.8622 (p) cc_final: 0.8415 (m) REVERT: Z 115 ILE cc_start: 0.9013 (mt) cc_final: 0.8800 (mp) REVERT: Z 124 TYR cc_start: 0.8350 (t80) cc_final: 0.7946 (t80) REVERT: Z 161 LEU cc_start: 0.8543 (tp) cc_final: 0.8324 (tp) REVERT: 0 133 ASN cc_start: 0.7968 (m-40) cc_final: 0.7629 (m-40) REVERT: 0 149 THR cc_start: 0.9530 (m) cc_final: 0.9305 (t) REVERT: 4 117 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.7870 (pp) REVERT: 4 150 PHE cc_start: 0.9038 (p90) cc_final: 0.8415 (p90) REVERT: 4 151 TYR cc_start: 0.8254 (t80) cc_final: 0.7576 (t80) REVERT: 6 127 GLN cc_start: 0.8904 (tp40) cc_final: 0.8424 (tp40) REVERT: 6 149 THR cc_start: 0.9167 (m) cc_final: 0.8414 (p) REVERT: 6 168 LEU cc_start: 0.9140 (tp) cc_final: 0.8850 (tt) REVERT: 8 115 ILE cc_start: 0.9094 (mt) cc_final: 0.8789 (mm) REVERT: 8 144 ASN cc_start: 0.8104 (t0) cc_final: 0.7642 (t0) REVERT: x 112 SER cc_start: 0.8674 (p) cc_final: 0.8266 (m) REVERT: x 117 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6936 (pp) REVERT: x 150 PHE cc_start: 0.9413 (p90) cc_final: 0.8466 (p90) REVERT: y 115 ILE cc_start: 0.9432 (mt) cc_final: 0.9112 (mt) REVERT: y 117 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8714 (pp) REVERT: y 148 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7068 (mtmm) REVERT: y 160 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7811 (mm-30) REVERT: z 112 SER cc_start: 0.9134 (p) cc_final: 0.8708 (m) REVERT: z 119 ASN cc_start: 0.8510 (m-40) cc_final: 0.8220 (p0) REVERT: z 148 LYS cc_start: 0.9000 (mppt) cc_final: 0.8679 (mtmt) REVERT: z 149 THR cc_start: 0.9162 (m) cc_final: 0.8675 (t) REVERT: z 151 TYR cc_start: 0.8587 (t80) cc_final: 0.8273 (t80) REVERT: z 161 LEU cc_start: 0.8891 (tp) cc_final: 0.8649 (tt) REVERT: 1 117 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6534 (pp) REVERT: 1 127 GLN cc_start: 0.7963 (tp40) cc_final: 0.7466 (tp40) REVERT: 1 133 ASN cc_start: 0.8690 (m-40) cc_final: 0.8338 (t0) REVERT: 1 147 ASP cc_start: 0.8283 (t0) cc_final: 0.8013 (m-30) REVERT: 1 148 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8148 (mtpp) REVERT: 3 115 ILE cc_start: 0.8836 (mt) cc_final: 0.8130 (mt) REVERT: 3 125 LEU cc_start: 0.9252 (tp) cc_final: 0.9050 (tt) REVERT: 3 129 LEU cc_start: 0.8895 (mt) cc_final: 0.8611 (mp) REVERT: 5 112 SER cc_start: 0.8492 (p) cc_final: 0.8022 (m) REVERT: 5 117 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7660 (pp) REVERT: 5 127 GLN cc_start: 0.8868 (tp40) cc_final: 0.8578 (tp40) REVERT: 7 112 SER cc_start: 0.9031 (p) cc_final: 0.8706 (m) REVERT: 9 128 TYR cc_start: 0.8836 (t80) cc_final: 0.8554 (t80) REVERT: a 24 GLN cc_start: 0.8371 (tp40) cc_final: 0.7939 (tp40) REVERT: a 26 LEU cc_start: 0.9127 (tp) cc_final: 0.8845 (tp) REVERT: a 53 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8106 (mmtp) REVERT: a 60 TYR cc_start: 0.8548 (t80) cc_final: 0.7621 (t80) REVERT: a 61 ARG cc_start: 0.9362 (mmt180) cc_final: 0.9116 (mmt-90) REVERT: a 72 LYS cc_start: 0.9561 (tmtt) cc_final: 0.9275 (tptp) REVERT: a 80 GLN cc_start: 0.8587 (mt0) cc_final: 0.8182 (tm-30) REVERT: b 43 ASN cc_start: 0.8465 (t0) cc_final: 0.8152 (t0) REVERT: b 45 GLN cc_start: 0.8659 (tp40) cc_final: 0.7718 (tm-30) REVERT: c 19 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8094 (m-80) REVERT: c 69 LYS cc_start: 0.9354 (tptm) cc_final: 0.9092 (tptt) REVERT: d 20 ASP cc_start: 0.7870 (m-30) cc_final: 0.7581 (m-30) REVERT: d 36 LYS cc_start: 0.8713 (mttt) cc_final: 0.8487 (mttt) REVERT: d 50 TYR cc_start: 0.9078 (t80) cc_final: 0.8736 (t80) REVERT: d 57 TYR cc_start: 0.8967 (t80) cc_final: 0.8660 (t80) REVERT: f 21 ASP cc_start: 0.8419 (m-30) cc_final: 0.7125 (m-30) REVERT: f 60 TYR cc_start: 0.8308 (t80) cc_final: 0.7720 (t80) REVERT: f 75 ASP cc_start: 0.8009 (m-30) cc_final: 0.7776 (m-30) REVERT: g 14 SER cc_start: 0.8914 (m) cc_final: 0.8674 (p) REVERT: g 19 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8294 (t80) REVERT: g 25 THR cc_start: 0.8507 (p) cc_final: 0.8145 (p) REVERT: g 26 LEU cc_start: 0.9193 (tt) cc_final: 0.8833 (tt) REVERT: g 65 SER cc_start: 0.9047 (m) cc_final: 0.8822 (t) REVERT: g 79 ILE cc_start: 0.9285 (mm) cc_final: 0.9055 (mm) REVERT: h 19 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7937 (t80) REVERT: h 66 ASN cc_start: 0.9357 (m-40) cc_final: 0.9067 (m-40) REVERT: i 19 PHE cc_start: 0.8889 (OUTLIER) cc_final: 0.8387 (t80) REVERT: i 50 TYR cc_start: 0.9278 (t80) cc_final: 0.9000 (t80) REVERT: i 81 ASN cc_start: 0.9352 (m-40) cc_final: 0.9051 (m-40) REVERT: j 13 SER cc_start: 0.9308 (p) cc_final: 0.9089 (m) REVERT: j 25 THR cc_start: 0.8219 (p) cc_final: 0.7692 (t) REVERT: j 26 LEU cc_start: 0.9044 (tp) cc_final: 0.8726 (tp) REVERT: j 55 SER cc_start: 0.9279 (m) cc_final: 0.8901 (p) REVERT: k 13 SER cc_start: 0.8856 (p) cc_final: 0.8172 (t) REVERT: k 37 LEU cc_start: 0.9087 (tp) cc_final: 0.8783 (tt) REVERT: k 50 TYR cc_start: 0.9096 (t80) cc_final: 0.8782 (t80) REVERT: k 64 GLN cc_start: 0.9400 (tt0) cc_final: 0.9054 (tt0) REVERT: k 72 LYS cc_start: 0.8972 (tmtp) cc_final: 0.8571 (tmmt) REVERT: k 81 ASN cc_start: 0.9170 (m-40) cc_final: 0.8871 (m-40) REVERT: l 25 THR cc_start: 0.8920 (p) cc_final: 0.8175 (p) REVERT: l 36 LYS cc_start: 0.8960 (mtpp) cc_final: 0.8552 (mtpp) REVERT: l 43 ASN cc_start: 0.8396 (t0) cc_final: 0.8170 (t0) REVERT: l 45 GLN cc_start: 0.7777 (tp40) cc_final: 0.7391 (tp40) REVERT: l 50 TYR cc_start: 0.9148 (t80) cc_final: 0.8740 (t80) REVERT: m 14 SER cc_start: 0.9324 (m) cc_final: 0.8987 (t) REVERT: m 20 ASP cc_start: 0.8104 (m-30) cc_final: 0.7629 (m-30) REVERT: m 75 ASP cc_start: 0.8146 (m-30) cc_final: 0.7689 (m-30) REVERT: n 3 VAL cc_start: 0.8611 (t) cc_final: 0.8241 (m) REVERT: n 53 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8915 (mmtm) REVERT: n 75 ASP cc_start: 0.8372 (m-30) cc_final: 0.7838 (m-30) REVERT: n 80 GLN cc_start: 0.8609 (tm-30) cc_final: 0.7714 (tm-30) REVERT: o 43 ASN cc_start: 0.7823 (t0) cc_final: 0.7384 (t0) REVERT: o 50 TYR cc_start: 0.9135 (t80) cc_final: 0.8645 (t80) REVERT: o 75 ASP cc_start: 0.8507 (m-30) cc_final: 0.8292 (m-30) REVERT: p 12 LEU cc_start: 0.9513 (mt) cc_final: 0.9056 (mt) REVERT: p 14 SER cc_start: 0.8856 (m) cc_final: 0.8548 (p) REVERT: p 45 GLN cc_start: 0.8153 (tp40) cc_final: 0.7161 (mm-40) REVERT: p 58 THR cc_start: 0.9564 (m) cc_final: 0.9360 (p) REVERT: p 75 ASP cc_start: 0.8637 (m-30) cc_final: 0.8238 (m-30) REVERT: q 14 SER cc_start: 0.9333 (m) cc_final: 0.9028 (p) REVERT: q 19 PHE cc_start: 0.7951 (m-80) cc_final: 0.7672 (m-80) REVERT: q 32 LEU cc_start: 0.8506 (tp) cc_final: 0.8183 (tp) REVERT: q 36 LYS cc_start: 0.8693 (mttt) cc_final: 0.8429 (mtmt) REVERT: q 64 GLN cc_start: 0.9017 (tt0) cc_final: 0.8741 (tt0) REVERT: r 14 SER cc_start: 0.9145 (m) cc_final: 0.8939 (p) REVERT: s 7 ASN cc_start: 0.6944 (m-40) cc_final: 0.5819 (p0) REVERT: s 23 THR cc_start: 0.8699 (m) cc_final: 0.8160 (p) REVERT: s 27 GLN cc_start: 0.8430 (mt0) cc_final: 0.7712 (tm-30) REVERT: s 37 LEU cc_start: 0.8884 (tt) cc_final: 0.8488 (tt) REVERT: s 65 SER cc_start: 0.8983 (t) cc_final: 0.8634 (m) REVERT: s 69 LYS cc_start: 0.8420 (tptm) cc_final: 0.7437 (ttmt) REVERT: s 75 ASP cc_start: 0.7483 (m-30) cc_final: 0.7238 (m-30) REVERT: t 26 LEU cc_start: 0.8251 (mt) cc_final: 0.7764 (mt) REVERT: t 47 LEU cc_start: 0.9032 (mt) cc_final: 0.8826 (mt) REVERT: t 51 GLN cc_start: 0.8916 (tt0) cc_final: 0.7000 (mm-40) REVERT: t 69 LYS cc_start: 0.9132 (tptm) cc_final: 0.8549 (mttt) REVERT: u 15 LEU cc_start: 0.9185 (mt) cc_final: 0.8864 (tp) REVERT: u 26 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8960 (mt) REVERT: u 30 LEU cc_start: 0.8742 (tp) cc_final: 0.8506 (tt) REVERT: u 49 GLU cc_start: 0.7636 (mm-30) cc_final: 0.7332 (mm-30) REVERT: u 69 LYS cc_start: 0.9102 (tptm) cc_final: 0.7645 (ttmt) REVERT: u 75 ASP cc_start: 0.8334 (m-30) cc_final: 0.8060 (m-30) REVERT: u 78 ILE cc_start: 0.9477 (mt) cc_final: 0.9248 (mt) REVERT: u 82 PHE cc_start: 0.9211 (m-10) cc_final: 0.8999 (m-80) REVERT: v 15 LEU cc_start: 0.9371 (mt) cc_final: 0.9101 (tp) REVERT: v 27 GLN cc_start: 0.8066 (mt0) cc_final: 0.7585 (tt0) REVERT: v 32 LEU cc_start: 0.9247 (tp) cc_final: 0.8932 (tp) REVERT: v 36 LYS cc_start: 0.8939 (mttt) cc_final: 0.8584 (mttm) REVERT: v 68 VAL cc_start: 0.9546 (t) cc_final: 0.9329 (m) REVERT: v 69 LYS cc_start: 0.8922 (tptm) cc_final: 0.8288 (mttm) REVERT: w 61 ARG cc_start: 0.8701 (mmt180) cc_final: 0.7208 (ttt180) REVERT: w 71 ILE cc_start: 0.9381 (mm) cc_final: 0.8621 (mm) REVERT: w 72 LYS cc_start: 0.9193 (tmtt) cc_final: 0.8540 (tptp) REVERT: w 75 ASP cc_start: 0.8255 (m-30) cc_final: 0.7457 (m-30) REVERT: a0 103 LYS cc_start: 0.8009 (tttm) cc_final: 0.7015 (tptt) REVERT: d0 103 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8099 (tttt) REVERT: e0 103 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8390 (tttt) REVERT: f0 103 LYS cc_start: 0.9376 (ttmt) cc_final: 0.8412 (tptt) REVERT: g0 103 LYS cc_start: 0.8992 (mtmt) cc_final: 0.7557 (tptt) REVERT: i0 90 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.4181 (p90) REVERT: i0 93 ASP cc_start: 0.7733 (p0) cc_final: 0.7526 (p0) REVERT: i0 103 LYS cc_start: 0.8993 (tttt) cc_final: 0.8667 (tptt) REVERT: k0 103 LYS cc_start: 0.8695 (ttmm) cc_final: 0.8126 (tptt) REVERT: l0 103 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8096 (tptt) REVERT: n0 97 SER cc_start: 0.9039 (m) cc_final: 0.8775 (p) REVERT: n0 103 LYS cc_start: 0.8949 (ttmt) cc_final: 0.8428 (ttpt) REVERT: p0 103 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8165 (tptt) REVERT: q0 103 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8361 (tptt) REVERT: r0 102 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7995 (mt-10) REVERT: r0 103 LYS cc_start: 0.8883 (ttmt) cc_final: 0.7630 (tptt) REVERT: t0 103 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8188 (tptt) REVERT: t0 105 ARG cc_start: 0.9177 (ttm110) cc_final: 0.8017 (tpm170) REVERT: u0 98 SER cc_start: 0.9091 (m) cc_final: 0.8403 (p) REVERT: u0 100 ARG cc_start: 0.8017 (ttm110) cc_final: 0.7369 (tpt170) REVERT: u0 103 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8050 (tptt) REVERT: v0 92 THR cc_start: 0.8375 (m) cc_final: 0.8137 (m) REVERT: v0 100 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7458 (tpt170) REVERT: v0 103 LYS cc_start: 0.9309 (mttt) cc_final: 0.8095 (tptt) REVERT: w0 103 LYS cc_start: 0.8981 (ttmt) cc_final: 0.8509 (tptt) REVERT: x0 103 LYS cc_start: 0.8489 (ttmt) cc_final: 0.7724 (tptt) outliers start: 164 outliers final: 62 residues processed: 2665 average time/residue: 0.5345 time to fit residues: 2391.6116 Evaluate side-chains 2093 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 2005 time to evaluate : 5.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 441 optimal weight: 4.9990 chunk 396 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 267 optimal weight: 0.6980 chunk 211 optimal weight: 0.1980 chunk 409 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 249 optimal weight: 0.9990 chunk 305 optimal weight: 0.2980 chunk 474 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 49 ASN A 77 ASN B 210 GLN D 106 HIS ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN F 11 HIS F 119 ASN ** F 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 247 HIS F 252 ASN I 76 HIS ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 44 GLN P 59 ASN T 80 GLN U 80 GLN W 81 ASN ** X 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 133 ASN 4 119 ASN 4 137 HIS 6 133 ASN x 123 ASN y 123 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 64 GLN a 66 ASN b 64 GLN ** c 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 ASN ** f 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 81 ASN ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** l 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 62 ASN m 64 GLN n 81 ASN p 64 GLN p 80 GLN q 80 GLN r 27 GLN r 64 GLN ** r 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 81 ASN v 80 GLN v 81 ASN w 64 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 44858 Z= 0.213 Angle : 0.604 9.770 60890 Z= 0.302 Chirality : 0.040 0.184 7369 Planarity : 0.004 0.064 7620 Dihedral : 4.093 83.880 5953 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.40 % Allowed : 2.57 % Favored : 97.03 % 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: 3.35 (0.12), residues: 5404 helix: 3.36 (0.08), residues: 4159 sheet: 1.88 (0.33), residues: 192 loop : -2.97 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 174 HIS 0.011 0.001 HIS I 76 PHE 0.032 0.002 PHE c 19 TYR 0.028 0.002 TYR o 60 ARG 0.008 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2392 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 2372 time to evaluate : 5.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8643 (p) cc_final: 0.8116 (p) REVERT: A 36 MET cc_start: 0.8914 (ttp) cc_final: 0.8358 (ttm) REVERT: A 69 GLU cc_start: 0.7623 (tp30) cc_final: 0.7036 (mm-30) REVERT: A 97 MET cc_start: 0.8445 (tpt) cc_final: 0.8094 (tpt) REVERT: A 101 GLN cc_start: 0.8800 (tt0) cc_final: 0.8410 (tm-30) REVERT: A 142 TYR cc_start: 0.9186 (t80) cc_final: 0.8713 (t80) REVERT: A 177 MET cc_start: 0.7916 (ptp) cc_final: 0.7601 (mtm) REVERT: A 205 LYS cc_start: 0.8948 (mttt) cc_final: 0.8289 (tttt) REVERT: B 120 GLU cc_start: 0.6417 (mt-10) cc_final: 0.5721 (mp0) REVERT: B 177 MET cc_start: 0.7960 (mtt) cc_final: 0.7537 (mtt) REVERT: B 190 LYS cc_start: 0.9235 (mtmt) cc_final: 0.8681 (mtmm) REVERT: C 105 LYS cc_start: 0.9163 (tttp) cc_final: 0.8754 (mtpt) REVERT: C 117 ARG cc_start: 0.8513 (mtt180) cc_final: 0.8085 (tpt170) REVERT: C 146 GLU cc_start: 0.8681 (tp30) cc_final: 0.8194 (mm-30) REVERT: C 164 VAL cc_start: 0.9528 (t) cc_final: 0.9300 (t) REVERT: D 2 LEU cc_start: 0.9212 (mt) cc_final: 0.8950 (mt) REVERT: D 6 SER cc_start: 0.8850 (m) cc_final: 0.8134 (p) REVERT: D 133 TYR cc_start: 0.8532 (m-10) cc_final: 0.8044 (m-10) REVERT: D 177 MET cc_start: 0.8299 (mtt) cc_final: 0.8096 (mtt) REVERT: E 59 MET cc_start: 0.8423 (mtp) cc_final: 0.8130 (mtm) REVERT: E 64 MET cc_start: 0.8661 (mmm) cc_final: 0.7532 (mmm) REVERT: E 179 MET cc_start: 0.8624 (mmp) cc_final: 0.8365 (mmp) REVERT: E 194 PHE cc_start: 0.9027 (t80) cc_final: 0.8787 (t80) REVERT: F 101 SER cc_start: 0.9359 (m) cc_final: 0.9012 (t) REVERT: F 133 PHE cc_start: 0.8884 (t80) cc_final: 0.8525 (t80) REVERT: F 139 LEU cc_start: 0.9266 (tp) cc_final: 0.9040 (tp) REVERT: F 152 GLN cc_start: 0.9153 (tt0) cc_final: 0.8500 (tp-100) REVERT: F 202 VAL cc_start: 0.8920 (t) cc_final: 0.8574 (t) REVERT: G 5 VAL cc_start: 0.9316 (p) cc_final: 0.8914 (p) REVERT: G 75 CYS cc_start: 0.8616 (m) cc_final: 0.8303 (m) REVERT: G 79 MET cc_start: 0.8580 (mmm) cc_final: 0.8027 (mmm) REVERT: H 81 LEU cc_start: 0.8700 (mt) cc_final: 0.8421 (mt) REVERT: I 5 VAL cc_start: 0.9196 (t) cc_final: 0.8641 (p) REVERT: I 9 ASN cc_start: 0.8379 (m-40) cc_final: 0.8153 (m-40) REVERT: J 1 MET cc_start: 0.7700 (mmp) cc_final: 0.7488 (mmp) REVERT: J 3 ASP cc_start: 0.7471 (p0) cc_final: 0.7257 (p0) REVERT: J 66 TRP cc_start: 0.9138 (t60) cc_final: 0.8650 (t-100) REVERT: K 32 VAL cc_start: 0.6887 (t) cc_final: 0.6614 (t) REVERT: K 51 MET cc_start: 0.7653 (mmt) cc_final: 0.6413 (mmt) REVERT: K 174 TRP cc_start: 0.9329 (m100) cc_final: 0.9039 (m100) REVERT: K 176 ARG cc_start: 0.8532 (tpt-90) cc_final: 0.8324 (tpt-90) REVERT: N 46 SER cc_start: 0.8985 (m) cc_final: 0.8739 (p) REVERT: N 58 LEU cc_start: 0.9221 (mt) cc_final: 0.8958 (mt) REVERT: P 12 ILE cc_start: 0.8476 (mt) cc_final: 0.8033 (mt) REVERT: P 56 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7308 (tm-30) REVERT: P 57 SER cc_start: 0.9255 (m) cc_final: 0.8586 (p) REVERT: Q 13 ILE cc_start: 0.7972 (mt) cc_final: 0.7729 (mt) REVERT: Q 41 THR cc_start: 0.9311 (p) cc_final: 0.9101 (m) REVERT: Q 65 LYS cc_start: 0.8885 (mmtt) cc_final: 0.8325 (mptt) REVERT: U 43 ASN cc_start: 0.8837 (t0) cc_final: 0.8408 (t0) REVERT: U 46 LEU cc_start: 0.9094 (mp) cc_final: 0.8438 (tt) REVERT: V 32 LEU cc_start: 0.8654 (mt) cc_final: 0.8297 (tt) REVERT: V 64 GLN cc_start: 0.8541 (tt0) cc_final: 0.8340 (tt0) REVERT: W 39 LYS cc_start: 0.8296 (mttt) cc_final: 0.7760 (mptt) REVERT: W 43 ASN cc_start: 0.8716 (t0) cc_final: 0.8036 (t0) REVERT: X 117 LEU cc_start: 0.7719 (pp) cc_final: 0.7195 (mt) REVERT: X 142 ARG cc_start: 0.8274 (mmt-90) cc_final: 0.7788 (mmt-90) REVERT: Y 112 SER cc_start: 0.7606 (p) cc_final: 0.7363 (m) REVERT: Y 123 ASN cc_start: 0.8666 (t0) cc_final: 0.8379 (t0) REVERT: Y 127 GLN cc_start: 0.7874 (tm-30) cc_final: 0.6803 (tm-30) REVERT: 0 126 ILE cc_start: 0.9225 (mt) cc_final: 0.8997 (mt) REVERT: 4 150 PHE cc_start: 0.9092 (p90) cc_final: 0.8571 (p90) REVERT: 4 151 TYR cc_start: 0.8300 (t80) cc_final: 0.7719 (t80) REVERT: 6 127 GLN cc_start: 0.8977 (tp40) cc_final: 0.8340 (tp40) REVERT: 6 138 ARG cc_start: 0.8443 (mtp85) cc_final: 0.7354 (mtm110) REVERT: 6 149 THR cc_start: 0.8984 (m) cc_final: 0.8017 (p) REVERT: 8 111 ILE cc_start: 0.9295 (mt) cc_final: 0.9054 (mt) REVERT: 8 115 ILE cc_start: 0.8951 (mt) cc_final: 0.8670 (mm) REVERT: 8 144 ASN cc_start: 0.8151 (t0) cc_final: 0.7620 (t0) REVERT: x 112 SER cc_start: 0.8655 (p) cc_final: 0.8291 (m) REVERT: x 149 THR cc_start: 0.9352 (t) cc_final: 0.8999 (p) REVERT: x 150 PHE cc_start: 0.9322 (p90) cc_final: 0.8541 (p90) REVERT: x 158 LEU cc_start: 0.8443 (tp) cc_final: 0.8136 (mm) REVERT: x 168 LEU cc_start: 0.9443 (tp) cc_final: 0.9034 (tp) REVERT: y 115 ILE cc_start: 0.9355 (mt) cc_final: 0.9125 (mt) REVERT: y 158 LEU cc_start: 0.8221 (tp) cc_final: 0.7928 (mm) REVERT: y 160 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7919 (mm-30) REVERT: z 112 SER cc_start: 0.9103 (p) cc_final: 0.8660 (m) REVERT: z 119 ASN cc_start: 0.8673 (m-40) cc_final: 0.8211 (p0) REVERT: z 139 TYR cc_start: 0.8130 (m-80) cc_final: 0.7870 (m-80) REVERT: z 149 THR cc_start: 0.8967 (m) cc_final: 0.8620 (t) REVERT: z 151 TYR cc_start: 0.8648 (t80) cc_final: 0.8379 (t80) REVERT: 1 130 LYS cc_start: 0.8270 (mmtp) cc_final: 0.8034 (mmtp) REVERT: 1 133 ASN cc_start: 0.8674 (m-40) cc_final: 0.8230 (t0) REVERT: 1 148 LYS cc_start: 0.8750 (mtpt) cc_final: 0.8128 (mtpp) REVERT: 3 115 ILE cc_start: 0.8842 (mt) cc_final: 0.8196 (mt) REVERT: 5 112 SER cc_start: 0.8272 (p) cc_final: 0.8039 (m) REVERT: 7 160 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8274 (mm-30) REVERT: a 24 GLN cc_start: 0.8275 (tp40) cc_final: 0.7979 (tp40) REVERT: a 26 LEU cc_start: 0.9105 (tp) cc_final: 0.8761 (tp) REVERT: a 60 TYR cc_start: 0.8670 (t80) cc_final: 0.7393 (t80) REVERT: a 72 LYS cc_start: 0.9545 (tmtt) cc_final: 0.9317 (tptp) REVERT: b 43 ASN cc_start: 0.8365 (t0) cc_final: 0.8124 (t0) REVERT: b 45 GLN cc_start: 0.8497 (tp40) cc_final: 0.7727 (tm-30) REVERT: b 49 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7236 (mm-30) REVERT: b 59 LEU cc_start: 0.9509 (mp) cc_final: 0.9305 (mp) REVERT: b 65 SER cc_start: 0.9265 (m) cc_final: 0.8667 (t) REVERT: c 9 ASP cc_start: 0.8569 (t0) cc_final: 0.8217 (t0) REVERT: c 82 PHE cc_start: 0.8843 (m-10) cc_final: 0.8517 (m-10) REVERT: d 50 TYR cc_start: 0.9061 (t80) cc_final: 0.8645 (t80) REVERT: d 57 TYR cc_start: 0.9077 (t80) cc_final: 0.8710 (t80) REVERT: d 71 ILE cc_start: 0.8848 (mm) cc_final: 0.8423 (mm) REVERT: d 75 ASP cc_start: 0.8528 (m-30) cc_final: 0.8177 (m-30) REVERT: f 17 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7133 (tm-30) REVERT: f 75 ASP cc_start: 0.8222 (m-30) cc_final: 0.7990 (m-30) REVERT: g 14 SER cc_start: 0.8667 (m) cc_final: 0.8369 (p) REVERT: g 25 THR cc_start: 0.8336 (p) cc_final: 0.8055 (p) REVERT: g 54 LEU cc_start: 0.9191 (tp) cc_final: 0.8980 (tp) REVERT: g 72 LYS cc_start: 0.9402 (tmtt) cc_final: 0.9200 (tptm) REVERT: g 79 ILE cc_start: 0.9161 (mm) cc_final: 0.8959 (mm) REVERT: h 25 THR cc_start: 0.7450 (t) cc_final: 0.7142 (t) REVERT: h 29 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8118 (mt-10) REVERT: h 59 LEU cc_start: 0.9398 (mt) cc_final: 0.9189 (mt) REVERT: h 66 ASN cc_start: 0.9293 (m-40) cc_final: 0.9086 (m110) REVERT: i 25 THR cc_start: 0.8001 (p) cc_final: 0.7766 (p) REVERT: i 50 TYR cc_start: 0.9271 (t80) cc_final: 0.9004 (t80) REVERT: i 80 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7857 (tm-30) REVERT: j 14 SER cc_start: 0.9124 (m) cc_final: 0.8374 (t) REVERT: j 25 THR cc_start: 0.8498 (p) cc_final: 0.7978 (t) REVERT: j 55 SER cc_start: 0.9151 (m) cc_final: 0.8878 (p) REVERT: k 13 SER cc_start: 0.8797 (p) cc_final: 0.8539 (t) REVERT: k 50 TYR cc_start: 0.9236 (t80) cc_final: 0.8985 (t80) REVERT: k 72 LYS cc_start: 0.8862 (tttp) cc_final: 0.8578 (tttt) REVERT: l 20 ASP cc_start: 0.7916 (m-30) cc_final: 0.7432 (m-30) REVERT: l 25 THR cc_start: 0.8857 (p) cc_final: 0.8065 (p) REVERT: l 45 GLN cc_start: 0.7913 (tp40) cc_final: 0.7330 (tp40) REVERT: l 50 TYR cc_start: 0.9233 (t80) cc_final: 0.8835 (t80) REVERT: m 14 SER cc_start: 0.9145 (m) cc_final: 0.8945 (t) REVERT: m 20 ASP cc_start: 0.8114 (m-30) cc_final: 0.7757 (m-30) REVERT: m 43 ASN cc_start: 0.6984 (t0) cc_final: 0.6780 (t0) REVERT: m 50 TYR cc_start: 0.8683 (t80) cc_final: 0.8306 (t80) REVERT: m 75 ASP cc_start: 0.8249 (m-30) cc_final: 0.7632 (m-30) REVERT: n 3 VAL cc_start: 0.8611 (t) cc_final: 0.8229 (m) REVERT: n 53 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8884 (mmtm) REVERT: n 75 ASP cc_start: 0.8449 (m-30) cc_final: 0.8126 (m-30) REVERT: n 80 GLN cc_start: 0.8697 (tm-30) cc_final: 0.7906 (tm-30) REVERT: o 14 SER cc_start: 0.8780 (t) cc_final: 0.8273 (p) REVERT: o 37 LEU cc_start: 0.9045 (tp) cc_final: 0.8822 (tt) REVERT: o 43 ASN cc_start: 0.7576 (t0) cc_final: 0.7262 (t0) REVERT: o 50 TYR cc_start: 0.9301 (t80) cc_final: 0.8902 (t80) REVERT: o 75 ASP cc_start: 0.8651 (m-30) cc_final: 0.8367 (t0) REVERT: p 12 LEU cc_start: 0.9328 (mt) cc_final: 0.9006 (mt) REVERT: p 14 SER cc_start: 0.8876 (m) cc_final: 0.8603 (p) REVERT: p 26 LEU cc_start: 0.8125 (mm) cc_final: 0.7857 (mm) REVERT: p 75 ASP cc_start: 0.8685 (m-30) cc_final: 0.8207 (m-30) REVERT: q 32 LEU cc_start: 0.8102 (tp) cc_final: 0.7739 (tp) REVERT: q 36 LYS cc_start: 0.8675 (mttt) cc_final: 0.8393 (mtmt) REVERT: r 8 ASP cc_start: 0.8248 (t0) cc_final: 0.7998 (t0) REVERT: s 7 ASN cc_start: 0.6549 (m-40) cc_final: 0.5579 (p0) REVERT: s 23 THR cc_start: 0.8679 (m) cc_final: 0.8312 (m) REVERT: s 27 GLN cc_start: 0.8425 (mt0) cc_final: 0.7744 (tm-30) REVERT: s 65 SER cc_start: 0.8962 (t) cc_final: 0.8712 (m) REVERT: s 69 LYS cc_start: 0.8530 (tptm) cc_final: 0.7447 (ttmt) REVERT: t 47 LEU cc_start: 0.8990 (mt) cc_final: 0.8758 (mt) REVERT: t 51 GLN cc_start: 0.8926 (tt0) cc_final: 0.7029 (mm-40) REVERT: t 55 SER cc_start: 0.9210 (m) cc_final: 0.9009 (p) REVERT: t 69 LYS cc_start: 0.9207 (tptm) cc_final: 0.8605 (mttt) REVERT: t 72 LYS cc_start: 0.9564 (tmtt) cc_final: 0.9350 (tttm) REVERT: t 75 ASP cc_start: 0.8694 (m-30) cc_final: 0.8484 (m-30) REVERT: u 15 LEU cc_start: 0.9082 (mt) cc_final: 0.8792 (tp) REVERT: u 20 ASP cc_start: 0.7453 (t0) cc_final: 0.7228 (t0) REVERT: u 30 LEU cc_start: 0.8819 (tp) cc_final: 0.8496 (tt) REVERT: u 49 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7369 (mm-30) REVERT: u 69 LYS cc_start: 0.9045 (tptm) cc_final: 0.7662 (ttmt) REVERT: u 72 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8691 (tmtt) REVERT: v 27 GLN cc_start: 0.7983 (mt0) cc_final: 0.7654 (tt0) REVERT: v 32 LEU cc_start: 0.9274 (tp) cc_final: 0.8967 (tp) REVERT: v 36 LYS cc_start: 0.8960 (mttt) cc_final: 0.8600 (mttm) REVERT: v 69 LYS cc_start: 0.9035 (tptm) cc_final: 0.8225 (mttm) REVERT: w 25 THR cc_start: 0.8459 (p) cc_final: 0.8067 (p) REVERT: w 57 TYR cc_start: 0.8791 (t80) cc_final: 0.8249 (t80) REVERT: w 61 ARG cc_start: 0.8425 (mmt180) cc_final: 0.6857 (ttt180) REVERT: w 69 LYS cc_start: 0.9231 (tppt) cc_final: 0.7752 (tppt) REVERT: w 72 LYS cc_start: 0.9157 (tmtt) cc_final: 0.8501 (tptp) REVERT: a0 103 LYS cc_start: 0.8289 (tttm) cc_final: 0.7126 (tptt) REVERT: d0 103 LYS cc_start: 0.9219 (ttmt) cc_final: 0.7869 (tptt) REVERT: e0 103 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8191 (tttt) REVERT: f0 103 LYS cc_start: 0.9374 (ttmt) cc_final: 0.8355 (tptt) REVERT: g0 103 LYS cc_start: 0.8932 (mtmt) cc_final: 0.7650 (tptt) REVERT: i0 93 ASP cc_start: 0.7819 (p0) cc_final: 0.7510 (p0) REVERT: i0 103 LYS cc_start: 0.8983 (tttt) cc_final: 0.8659 (tptt) REVERT: k0 103 LYS cc_start: 0.8743 (ttmm) cc_final: 0.8154 (tptt) REVERT: l0 103 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8155 (tptt) REVERT: n0 97 SER cc_start: 0.9043 (m) cc_final: 0.8652 (p) REVERT: n0 103 LYS cc_start: 0.8963 (ttmt) cc_final: 0.8437 (ttpt) REVERT: o0 102 GLU cc_start: 0.7302 (pt0) cc_final: 0.7063 (pp20) REVERT: p0 103 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8177 (tptt) REVERT: q0 103 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8347 (tptt) REVERT: r0 102 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8051 (mt-10) REVERT: r0 103 LYS cc_start: 0.8834 (ttmt) cc_final: 0.7596 (tptt) REVERT: t0 103 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8110 (tptt) REVERT: t0 105 ARG cc_start: 0.9178 (ttm110) cc_final: 0.8021 (tpm170) REVERT: u0 100 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7304 (tpt170) REVERT: u0 103 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8074 (tptt) REVERT: v0 92 THR cc_start: 0.8424 (m) cc_final: 0.8146 (m) REVERT: v0 103 LYS cc_start: 0.9297 (mttt) cc_final: 0.8022 (tptt) REVERT: w0 103 LYS cc_start: 0.8965 (ttmt) cc_final: 0.8495 (tptt) REVERT: x0 103 LYS cc_start: 0.8369 (ttmt) cc_final: 0.7705 (tptt) outliers start: 20 outliers final: 5 residues processed: 2378 average time/residue: 0.5420 time to fit residues: 2181.8056 Evaluate side-chains 2006 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2001 time to evaluate : 5.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 263 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 395 optimal weight: 1.9990 chunk 323 optimal weight: 0.0020 chunk 131 optimal weight: 0.0870 chunk 475 optimal weight: 2.9990 chunk 513 optimal weight: 0.0570 chunk 423 optimal weight: 1.9990 chunk 471 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 chunk 381 optimal weight: 0.7980 overall best weight: 0.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN E 44 GLN E 106 HIS F 11 HIS ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN ** F 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 HIS F 252 ASN K 162 GLN O 44 GLN T 80 GLN U 80 GLN ** Z 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 133 ASN 4 137 HIS ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN b 64 GLN ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN ** d 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 81 ASN ** f 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 51 GLN f 80 GLN g 80 GLN g 81 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 81 ASN k 64 GLN l 40 ASN ** m 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 7 ASN n 62 ASN n 81 ASN p 64 GLN p 80 GLN r 27 GLN r 64 GLN v 80 GLN v 81 ASN w 64 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 44858 Z= 0.180 Angle : 0.589 10.569 60890 Z= 0.291 Chirality : 0.039 0.187 7369 Planarity : 0.004 0.065 7620 Dihedral : 4.120 85.129 5953 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.18 % Allowed : 2.73 % Favored : 97.09 % 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: 3.31 (0.12), residues: 5404 helix: 3.32 (0.08), residues: 4150 sheet: 1.99 (0.32), residues: 192 loop : -2.89 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 66 HIS 0.008 0.001 HIS F 11 PHE 0.029 0.002 PHE F 28 TYR 0.024 0.001 TYR J 67 ARG 0.005 0.000 ARGv0 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2320 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2311 time to evaluate : 5.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8637 (p) cc_final: 0.7875 (p) REVERT: A 36 MET cc_start: 0.8901 (ttp) cc_final: 0.8407 (tpp) REVERT: A 68 ILE cc_start: 0.9522 (mt) cc_final: 0.9156 (mt) REVERT: A 69 GLU cc_start: 0.7656 (tp30) cc_final: 0.6941 (mm-30) REVERT: A 97 MET cc_start: 0.8356 (tpt) cc_final: 0.8022 (tpt) REVERT: A 101 GLN cc_start: 0.8633 (tt0) cc_final: 0.8388 (tm-30) REVERT: A 142 TYR cc_start: 0.9083 (t80) cc_final: 0.8670 (t80) REVERT: A 152 LYS cc_start: 0.9149 (tttt) cc_final: 0.8652 (ttmt) REVERT: A 205 LYS cc_start: 0.9145 (mttt) cc_final: 0.8231 (tttt) REVERT: A 209 GLU cc_start: 0.8051 (pt0) cc_final: 0.7800 (pt0) REVERT: B 67 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8217 (tt) REVERT: B 120 GLU cc_start: 0.6389 (mt-10) cc_final: 0.5760 (mp0) REVERT: B 146 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 177 MET cc_start: 0.8022 (mtt) cc_final: 0.7639 (mtt) REVERT: B 190 LYS cc_start: 0.9224 (mtmt) cc_final: 0.8444 (mtmm) REVERT: C 1 MET cc_start: 0.7162 (mmm) cc_final: 0.6627 (mmm) REVERT: C 25 THR cc_start: 0.9215 (p) cc_final: 0.8748 (t) REVERT: C 105 LYS cc_start: 0.9035 (tttp) cc_final: 0.8614 (mtpt) REVERT: C 117 ARG cc_start: 0.8459 (mtt180) cc_final: 0.8002 (tpt170) REVERT: C 146 GLU cc_start: 0.8597 (tp30) cc_final: 0.8317 (mm-30) REVERT: D 2 LEU cc_start: 0.9201 (mt) cc_final: 0.8957 (mt) REVERT: D 6 SER cc_start: 0.8831 (m) cc_final: 0.8106 (p) REVERT: D 156 TYR cc_start: 0.8661 (m-10) cc_final: 0.8103 (m-10) REVERT: D 177 MET cc_start: 0.8259 (mtt) cc_final: 0.8040 (mtt) REVERT: E 44 GLN cc_start: 0.8377 (mm110) cc_final: 0.8151 (mp10) REVERT: E 59 MET cc_start: 0.8410 (mtp) cc_final: 0.8143 (mtm) REVERT: E 64 MET cc_start: 0.8555 (mmm) cc_final: 0.7566 (mmm) REVERT: E 194 PHE cc_start: 0.9055 (t80) cc_final: 0.8848 (t80) REVERT: F 133 PHE cc_start: 0.8815 (t80) cc_final: 0.8389 (t80) REVERT: F 152 GLN cc_start: 0.9104 (tt0) cc_final: 0.8476 (tp-100) REVERT: F 170 ASN cc_start: 0.8342 (m-40) cc_final: 0.8057 (m-40) REVERT: F 202 VAL cc_start: 0.8922 (t) cc_final: 0.8712 (t) REVERT: G 5 VAL cc_start: 0.9173 (p) cc_final: 0.8845 (p) REVERT: G 75 CYS cc_start: 0.8542 (m) cc_final: 0.8304 (m) REVERT: G 79 MET cc_start: 0.8600 (mmm) cc_final: 0.7734 (mmm) REVERT: I 5 VAL cc_start: 0.9128 (t) cc_final: 0.8564 (p) REVERT: I 18 PHE cc_start: 0.8270 (m-80) cc_final: 0.7632 (m-80) REVERT: I 60 LEU cc_start: 0.8569 (mt) cc_final: 0.8368 (mt) REVERT: K 51 MET cc_start: 0.7578 (mmt) cc_final: 0.6519 (mmt) REVERT: K 132 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8154 (mttt) REVERT: K 140 LEU cc_start: 0.9063 (tp) cc_final: 0.8802 (tt) REVERT: N 58 LEU cc_start: 0.9239 (mt) cc_final: 0.8949 (mt) REVERT: O 41 THR cc_start: 0.8782 (t) cc_final: 0.8471 (m) REVERT: P 44 GLN cc_start: 0.8237 (tt0) cc_final: 0.7930 (tt0) REVERT: P 46 SER cc_start: 0.9491 (m) cc_final: 0.9111 (t) REVERT: P 56 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7300 (tm-30) REVERT: P 57 SER cc_start: 0.9054 (m) cc_final: 0.8543 (p) REVERT: Q 13 ILE cc_start: 0.7675 (mt) cc_final: 0.7382 (mt) REVERT: S 37 LEU cc_start: 0.9053 (tp) cc_final: 0.8618 (tp) REVERT: T 30 LEU cc_start: 0.9147 (tp) cc_final: 0.8850 (tp) REVERT: T 50 TYR cc_start: 0.9077 (t80) cc_final: 0.8872 (t80) REVERT: U 43 ASN cc_start: 0.8571 (t0) cc_final: 0.8312 (t0) REVERT: U 81 ASN cc_start: 0.9118 (m-40) cc_final: 0.8740 (m-40) REVERT: V 32 LEU cc_start: 0.8665 (mt) cc_final: 0.8336 (tt) REVERT: V 64 GLN cc_start: 0.8529 (tt0) cc_final: 0.8318 (tt0) REVERT: V 73 ASP cc_start: 0.8843 (t0) cc_final: 0.8638 (t0) REVERT: W 39 LYS cc_start: 0.8293 (mttt) cc_final: 0.7714 (mptt) REVERT: W 43 ASN cc_start: 0.8537 (t0) cc_final: 0.7969 (t0) REVERT: X 128 TYR cc_start: 0.8256 (t80) cc_final: 0.8035 (t80) REVERT: X 142 ARG cc_start: 0.8381 (mmt-90) cc_final: 0.7951 (mmt-90) REVERT: Y 112 SER cc_start: 0.7594 (p) cc_final: 0.7336 (m) REVERT: Y 123 ASN cc_start: 0.8747 (t0) cc_final: 0.8434 (t0) REVERT: Y 127 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7432 (tm-30) REVERT: Y 131 ASP cc_start: 0.7731 (m-30) cc_final: 0.7491 (m-30) REVERT: Z 142 ARG cc_start: 0.8177 (mmt-90) cc_final: 0.7916 (mmp80) REVERT: Z 158 LEU cc_start: 0.8854 (tt) cc_final: 0.8564 (mm) REVERT: Z 161 LEU cc_start: 0.8647 (tp) cc_final: 0.8419 (tp) REVERT: 2 167 THR cc_start: 0.8687 (t) cc_final: 0.8487 (t) REVERT: 4 131 ASP cc_start: 0.8250 (p0) cc_final: 0.8045 (p0) REVERT: 4 133 ASN cc_start: 0.7926 (t0) cc_final: 0.7680 (t0) REVERT: 4 150 PHE cc_start: 0.9174 (p90) cc_final: 0.8631 (p90) REVERT: 4 167 THR cc_start: 0.8773 (m) cc_final: 0.8539 (t) REVERT: 6 127 GLN cc_start: 0.8945 (tp40) cc_final: 0.8305 (tp40) REVERT: 6 138 ARG cc_start: 0.8388 (mtp85) cc_final: 0.7581 (mtm110) REVERT: 6 144 ASN cc_start: 0.8522 (m-40) cc_final: 0.8106 (m-40) REVERT: 8 111 ILE cc_start: 0.9299 (mt) cc_final: 0.9088 (mt) REVERT: 8 115 ILE cc_start: 0.8935 (mt) cc_final: 0.8645 (mm) REVERT: 8 144 ASN cc_start: 0.7858 (t0) cc_final: 0.7561 (t0) REVERT: x 112 SER cc_start: 0.8666 (p) cc_final: 0.8403 (m) REVERT: x 149 THR cc_start: 0.9352 (t) cc_final: 0.9003 (p) REVERT: x 150 PHE cc_start: 0.9357 (p90) cc_final: 0.8565 (p90) REVERT: x 153 SER cc_start: 0.9428 (t) cc_final: 0.9153 (p) REVERT: x 158 LEU cc_start: 0.8375 (tp) cc_final: 0.8076 (mm) REVERT: x 168 LEU cc_start: 0.9325 (tp) cc_final: 0.9024 (tp) REVERT: y 115 ILE cc_start: 0.9361 (mt) cc_final: 0.9131 (mt) REVERT: y 144 ASN cc_start: 0.8298 (t0) cc_final: 0.8055 (t0) REVERT: y 158 LEU cc_start: 0.8191 (tp) cc_final: 0.7852 (mm) REVERT: y 160 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7860 (mm-30) REVERT: y 164 ASN cc_start: 0.8595 (m-40) cc_final: 0.8309 (m-40) REVERT: z 112 SER cc_start: 0.9044 (p) cc_final: 0.8635 (m) REVERT: z 119 ASN cc_start: 0.8782 (m-40) cc_final: 0.8537 (m-40) REVERT: z 149 THR cc_start: 0.8953 (m) cc_final: 0.8614 (t) REVERT: z 151 TYR cc_start: 0.8601 (t80) cc_final: 0.8316 (t80) REVERT: 1 133 ASN cc_start: 0.8636 (m-40) cc_final: 0.8285 (t0) REVERT: 1 148 LYS cc_start: 0.8423 (mtpt) cc_final: 0.8083 (mtpp) REVERT: 3 115 ILE cc_start: 0.8709 (mt) cc_final: 0.8305 (mt) REVERT: 5 112 SER cc_start: 0.8242 (p) cc_final: 0.7995 (m) REVERT: 7 160 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8287 (mm-30) REVERT: 9 111 ILE cc_start: 0.9294 (mt) cc_final: 0.8980 (pt) REVERT: a 26 LEU cc_start: 0.9060 (tp) cc_final: 0.8760 (tp) REVERT: a 72 LYS cc_start: 0.9516 (tmtt) cc_final: 0.9264 (tptp) REVERT: b 45 GLN cc_start: 0.8481 (tp40) cc_final: 0.7645 (tm-30) REVERT: b 49 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7013 (mm-30) REVERT: b 65 SER cc_start: 0.9197 (m) cc_final: 0.8701 (t) REVERT: c 9 ASP cc_start: 0.8398 (t0) cc_final: 0.7999 (t0) REVERT: c 20 ASP cc_start: 0.8417 (t0) cc_final: 0.8017 (t0) REVERT: c 59 LEU cc_start: 0.9508 (mt) cc_final: 0.9014 (mt) REVERT: c 82 PHE cc_start: 0.8787 (m-10) cc_final: 0.8546 (m-10) REVERT: d 20 ASP cc_start: 0.8340 (m-30) cc_final: 0.8041 (m-30) REVERT: d 26 LEU cc_start: 0.8331 (mt) cc_final: 0.8109 (mt) REVERT: d 50 TYR cc_start: 0.9061 (t80) cc_final: 0.8641 (t80) REVERT: d 57 TYR cc_start: 0.9033 (t80) cc_final: 0.8598 (t80) REVERT: d 71 ILE cc_start: 0.8746 (mm) cc_final: 0.8351 (mm) REVERT: d 75 ASP cc_start: 0.8381 (m-30) cc_final: 0.8052 (m-30) REVERT: f 17 GLU cc_start: 0.7233 (tm-30) cc_final: 0.6951 (tm-30) REVERT: f 80 GLN cc_start: 0.8364 (tm130) cc_final: 0.7988 (tm-30) REVERT: g 14 SER cc_start: 0.8658 (m) cc_final: 0.8387 (p) REVERT: g 25 THR cc_start: 0.8175 (p) cc_final: 0.7920 (p) REVERT: g 54 LEU cc_start: 0.9168 (tp) cc_final: 0.8962 (tp) REVERT: g 72 LYS cc_start: 0.9338 (tmtt) cc_final: 0.9133 (tptm) REVERT: g 79 ILE cc_start: 0.9179 (mm) cc_final: 0.8897 (mm) REVERT: g 80 GLN cc_start: 0.8579 (tp-100) cc_final: 0.8337 (tm-30) REVERT: h 11 THR cc_start: 0.8841 (m) cc_final: 0.8038 (m) REVERT: i 50 TYR cc_start: 0.9238 (t80) cc_final: 0.8986 (t80) REVERT: i 80 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7851 (tm-30) REVERT: j 14 SER cc_start: 0.8940 (m) cc_final: 0.8318 (t) REVERT: j 80 GLN cc_start: 0.9058 (tp-100) cc_final: 0.8740 (tp-100) REVERT: k 13 SER cc_start: 0.8773 (p) cc_final: 0.8415 (t) REVERT: k 23 THR cc_start: 0.8773 (t) cc_final: 0.8565 (t) REVERT: k 43 ASN cc_start: 0.8145 (t0) cc_final: 0.7904 (t0) REVERT: k 50 TYR cc_start: 0.9242 (t80) cc_final: 0.8958 (t80) REVERT: l 16 SER cc_start: 0.8902 (m) cc_final: 0.8482 (m) REVERT: l 20 ASP cc_start: 0.7605 (m-30) cc_final: 0.7273 (m-30) REVERT: l 25 THR cc_start: 0.8914 (p) cc_final: 0.8273 (p) REVERT: l 45 GLN cc_start: 0.7646 (tp40) cc_final: 0.7445 (tp40) REVERT: l 50 TYR cc_start: 0.9173 (t80) cc_final: 0.8798 (t80) REVERT: l 57 TYR cc_start: 0.9162 (t80) cc_final: 0.8941 (t80) REVERT: m 20 ASP cc_start: 0.7722 (m-30) cc_final: 0.7405 (m-30) REVERT: m 24 GLN cc_start: 0.8208 (tp40) cc_final: 0.7697 (tp40) REVERT: m 43 ASN cc_start: 0.6965 (t0) cc_final: 0.6741 (t0) REVERT: m 50 TYR cc_start: 0.8719 (t80) cc_final: 0.8309 (t80) REVERT: m 75 ASP cc_start: 0.8432 (m-30) cc_final: 0.7813 (m-30) REVERT: n 3 VAL cc_start: 0.8546 (t) cc_final: 0.8207 (m) REVERT: n 29 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7112 (tm-30) REVERT: n 53 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8232 (mmtm) REVERT: n 58 THR cc_start: 0.9572 (m) cc_final: 0.9354 (t) REVERT: n 75 ASP cc_start: 0.8434 (m-30) cc_final: 0.8030 (m-30) REVERT: n 80 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8026 (tm-30) REVERT: o 14 SER cc_start: 0.8731 (t) cc_final: 0.8303 (p) REVERT: o 37 LEU cc_start: 0.8932 (tp) cc_final: 0.8690 (tt) REVERT: o 43 ASN cc_start: 0.7433 (t0) cc_final: 0.7192 (t0) REVERT: o 50 TYR cc_start: 0.9306 (t80) cc_final: 0.8696 (t80) REVERT: p 12 LEU cc_start: 0.9395 (mt) cc_final: 0.9004 (mt) REVERT: p 25 THR cc_start: 0.8381 (p) cc_final: 0.7562 (t) REVERT: p 26 LEU cc_start: 0.8113 (mm) cc_final: 0.7765 (mm) REVERT: p 46 LEU cc_start: 0.9289 (tp) cc_final: 0.9057 (tt) REVERT: p 75 ASP cc_start: 0.8698 (m-30) cc_final: 0.7859 (m-30) REVERT: q 23 THR cc_start: 0.8682 (t) cc_final: 0.8438 (m) REVERT: q 32 LEU cc_start: 0.8081 (tp) cc_final: 0.7772 (tp) REVERT: q 36 LYS cc_start: 0.8671 (mttt) cc_final: 0.8338 (mtmt) REVERT: r 59 LEU cc_start: 0.8779 (mt) cc_final: 0.8527 (mt) REVERT: s 7 ASN cc_start: 0.6670 (m-40) cc_final: 0.5796 (p0) REVERT: s 23 THR cc_start: 0.8660 (m) cc_final: 0.8325 (m) REVERT: s 24 GLN cc_start: 0.8157 (tp40) cc_final: 0.7798 (mm-40) REVERT: s 27 GLN cc_start: 0.8489 (mt0) cc_final: 0.7904 (tm-30) REVERT: s 65 SER cc_start: 0.8940 (t) cc_final: 0.8665 (m) REVERT: s 69 LYS cc_start: 0.8488 (tptm) cc_final: 0.7420 (ttmt) REVERT: t 26 LEU cc_start: 0.7848 (mt) cc_final: 0.7457 (mt) REVERT: t 47 LEU cc_start: 0.8947 (mt) cc_final: 0.8724 (mt) REVERT: t 51 GLN cc_start: 0.8730 (tt0) cc_final: 0.6619 (mm-40) REVERT: t 69 LYS cc_start: 0.9183 (tptm) cc_final: 0.8586 (mttt) REVERT: t 72 LYS cc_start: 0.9543 (tmtt) cc_final: 0.9332 (tttm) REVERT: t 75 ASP cc_start: 0.8661 (m-30) cc_final: 0.8412 (m-30) REVERT: u 30 LEU cc_start: 0.8789 (tp) cc_final: 0.8459 (tt) REVERT: u 49 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7436 (mm-30) REVERT: u 69 LYS cc_start: 0.8979 (tptm) cc_final: 0.7628 (ttmt) REVERT: u 72 LYS cc_start: 0.9120 (tmtt) cc_final: 0.8652 (tmtt) REVERT: u 75 ASP cc_start: 0.8963 (m-30) cc_final: 0.8246 (m-30) REVERT: v 27 GLN cc_start: 0.7909 (mt0) cc_final: 0.7677 (tp40) REVERT: v 32 LEU cc_start: 0.9221 (tp) cc_final: 0.8904 (tp) REVERT: v 36 LYS cc_start: 0.9005 (mttt) cc_final: 0.8656 (mttm) REVERT: v 69 LYS cc_start: 0.9090 (tptm) cc_final: 0.8155 (mttm) REVERT: w 25 THR cc_start: 0.8579 (p) cc_final: 0.8236 (p) REVERT: w 57 TYR cc_start: 0.8750 (t80) cc_final: 0.8294 (t80) REVERT: w 61 ARG cc_start: 0.8377 (mmt180) cc_final: 0.6769 (ttp-170) REVERT: a0 103 LYS cc_start: 0.8130 (tttm) cc_final: 0.7048 (tptt) REVERT: b0 96 VAL cc_start: 0.8200 (t) cc_final: 0.7865 (t) REVERT: d0 103 LYS cc_start: 0.9242 (ttmt) cc_final: 0.7837 (tptt) REVERT: e0 103 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8276 (tttt) REVERT: f0 103 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8309 (tptt) REVERT: g0 103 LYS cc_start: 0.8945 (mtmt) cc_final: 0.7647 (tptt) REVERT: i0 103 LYS cc_start: 0.8937 (tttt) cc_final: 0.8667 (tptt) REVERT: k0 103 LYS cc_start: 0.8708 (ttmm) cc_final: 0.8136 (tptt) REVERT: l0 103 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8121 (tptt) REVERT: n0 97 SER cc_start: 0.9058 (m) cc_final: 0.8796 (t) REVERT: n0 103 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8361 (ttpt) REVERT: p0 103 LYS cc_start: 0.8873 (ttpt) cc_final: 0.8066 (tptt) REVERT: q0 103 LYS cc_start: 0.8997 (ttmt) cc_final: 0.8314 (tptt) REVERT: r0 102 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8094 (mt-10) REVERT: r0 103 LYS cc_start: 0.8797 (ttmt) cc_final: 0.7537 (tptt) REVERT: t0 103 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8092 (tptt) REVERT: t0 105 ARG cc_start: 0.9157 (ttm110) cc_final: 0.8007 (tpm170) REVERT: u0 100 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7456 (tpt170) REVERT: u0 103 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8050 (tptt) REVERT: v0 92 THR cc_start: 0.8394 (m) cc_final: 0.8084 (m) REVERT: v0 103 LYS cc_start: 0.9230 (mttt) cc_final: 0.7809 (tptt) REVERT: w0 103 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8430 (tptt) REVERT: x0 103 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7723 (tptt) outliers start: 9 outliers final: 0 residues processed: 2313 average time/residue: 0.5056 time to fit residues: 1966.1445 Evaluate side-chains 1974 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1973 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 470 optimal weight: 0.9990 chunk 357 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 319 optimal weight: 1.9990 chunk 477 optimal weight: 3.9990 chunk 505 optimal weight: 0.2980 chunk 249 optimal weight: 0.9980 chunk 452 optimal weight: 0.0470 chunk 136 optimal weight: 2.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 210 GLN B 213 ASN E 44 GLN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN I 9 ASN K 162 GLN O 9 GLN O 44 GLN R 19 GLN R 44 GLN T 80 GLN U 80 GLN W 81 ASN 4 127 GLN 4 137 HIS y 123 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN b 43 ASN b 64 GLN ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 40 ASN f 43 ASN h 66 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 64 GLN p 80 GLN r 27 GLN r 64 GLN s 81 ASN v 81 ASN w 64 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 44858 Z= 0.199 Angle : 0.601 9.577 60890 Z= 0.296 Chirality : 0.039 0.289 7369 Planarity : 0.004 0.065 7620 Dihedral : 4.137 86.486 5953 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.14 % Allowed : 2.24 % Favored : 97.63 % 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: 3.17 (0.12), residues: 5404 helix: 3.22 (0.08), residues: 4151 sheet: 1.15 (0.33), residues: 224 loop : -2.92 (0.17), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 66 HIS 0.007 0.001 HIS F 11 PHE 0.027 0.002 PHE c 19 TYR 0.028 0.001 TYR h 60 ARG 0.006 0.000 ARGt0 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2245 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2238 time to evaluate : 5.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8124 (p) cc_final: 0.7287 (m) REVERT: A 36 MET cc_start: 0.8881 (ttp) cc_final: 0.8439 (ttm) REVERT: A 50 MET cc_start: 0.7997 (ttp) cc_final: 0.7774 (ttm) REVERT: A 68 ILE cc_start: 0.9541 (mt) cc_final: 0.9202 (mt) REVERT: A 69 GLU cc_start: 0.7635 (tp30) cc_final: 0.7182 (mm-30) REVERT: A 97 MET cc_start: 0.8410 (tpt) cc_final: 0.8197 (tpt) REVERT: A 101 GLN cc_start: 0.8735 (tt0) cc_final: 0.8449 (tm-30) REVERT: A 142 TYR cc_start: 0.9090 (t80) cc_final: 0.8757 (t80) REVERT: A 146 GLU cc_start: 0.9266 (mm-30) cc_final: 0.9040 (tp30) REVERT: A 152 LYS cc_start: 0.9139 (tttt) cc_final: 0.8664 (ttmt) REVERT: A 177 MET cc_start: 0.8116 (mtt) cc_final: 0.7889 (mtt) REVERT: A 205 LYS cc_start: 0.9040 (mttt) cc_final: 0.8143 (tttt) REVERT: A 209 GLU cc_start: 0.8017 (pt0) cc_final: 0.7754 (pt0) REVERT: B 65 LYS cc_start: 0.8632 (tttp) cc_final: 0.8256 (tmtt) REVERT: B 120 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5817 (mp0) REVERT: B 146 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7663 (mm-30) REVERT: B 177 MET cc_start: 0.8103 (mtt) cc_final: 0.7774 (mtt) REVERT: B 179 MET cc_start: 0.9150 (mmm) cc_final: 0.8737 (mmm) REVERT: B 190 LYS cc_start: 0.9249 (mtmt) cc_final: 0.8433 (mtmm) REVERT: C 25 THR cc_start: 0.9277 (p) cc_final: 0.8783 (t) REVERT: C 117 ARG cc_start: 0.8440 (mtt180) cc_final: 0.7976 (tpt170) REVERT: C 146 GLU cc_start: 0.8582 (tp30) cc_final: 0.8272 (mm-30) REVERT: C 178 MET cc_start: 0.8477 (mmp) cc_final: 0.8254 (mmm) REVERT: D 2 LEU cc_start: 0.9202 (mt) cc_final: 0.8938 (mt) REVERT: D 6 SER cc_start: 0.8773 (m) cc_final: 0.8043 (p) REVERT: D 27 TYR cc_start: 0.9046 (t80) cc_final: 0.8755 (t80) REVERT: D 156 TYR cc_start: 0.8637 (m-10) cc_final: 0.8118 (m-10) REVERT: E 64 MET cc_start: 0.8611 (mmm) cc_final: 0.7522 (mmm) REVERT: F 128 LYS cc_start: 0.8566 (ttpt) cc_final: 0.8342 (ttpt) REVERT: F 133 PHE cc_start: 0.8833 (t80) cc_final: 0.8359 (t80) REVERT: F 152 GLN cc_start: 0.9085 (tt0) cc_final: 0.8467 (tp-100) REVERT: F 170 ASN cc_start: 0.8355 (m110) cc_final: 0.8151 (m-40) REVERT: F 229 PHE cc_start: 0.8613 (t80) cc_final: 0.8323 (t80) REVERT: G 7 MET cc_start: 0.8481 (tpp) cc_final: 0.8173 (tpp) REVERT: G 52 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8435 (mtmt) REVERT: G 79 MET cc_start: 0.8508 (mmm) cc_final: 0.7992 (mmm) REVERT: H 35 LEU cc_start: 0.7961 (mp) cc_final: 0.7750 (mt) REVERT: H 77 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7839 (tm-30) REVERT: H 79 MET cc_start: 0.8131 (mmp) cc_final: 0.7623 (mmp) REVERT: I 5 VAL cc_start: 0.8855 (t) cc_final: 0.8609 (p) REVERT: I 18 PHE cc_start: 0.8275 (m-80) cc_final: 0.7559 (m-80) REVERT: I 53 LEU cc_start: 0.8043 (tp) cc_final: 0.7687 (tp) REVERT: I 60 LEU cc_start: 0.8588 (mt) cc_final: 0.8379 (mt) REVERT: K 32 VAL cc_start: 0.6863 (t) cc_final: 0.6638 (t) REVERT: K 51 MET cc_start: 0.7511 (mmt) cc_final: 0.7167 (mmt) REVERT: K 132 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8208 (mttt) REVERT: N 58 LEU cc_start: 0.9222 (mt) cc_final: 0.8886 (mt) REVERT: O 41 THR cc_start: 0.8729 (t) cc_final: 0.8438 (m) REVERT: P 44 GLN cc_start: 0.8195 (tt0) cc_final: 0.7904 (tt0) REVERT: P 56 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7155 (tm-30) REVERT: P 57 SER cc_start: 0.9123 (m) cc_final: 0.8554 (p) REVERT: Q 7 VAL cc_start: 0.8489 (m) cc_final: 0.8288 (t) REVERT: Q 13 ILE cc_start: 0.7675 (mt) cc_final: 0.7371 (mt) REVERT: S 25 THR cc_start: 0.7806 (t) cc_final: 0.7590 (t) REVERT: S 37 LEU cc_start: 0.9120 (tp) cc_final: 0.8728 (tp) REVERT: T 30 LEU cc_start: 0.9124 (tp) cc_final: 0.8854 (tp) REVERT: T 50 TYR cc_start: 0.9035 (t80) cc_final: 0.8822 (t80) REVERT: U 81 ASN cc_start: 0.9120 (m-40) cc_final: 0.8727 (m-40) REVERT: V 32 LEU cc_start: 0.8688 (mt) cc_final: 0.8332 (tt) REVERT: V 64 GLN cc_start: 0.8562 (tt0) cc_final: 0.8334 (tt0) REVERT: V 73 ASP cc_start: 0.8871 (t0) cc_final: 0.8630 (t0) REVERT: W 39 LYS cc_start: 0.8198 (mttt) cc_final: 0.7669 (mptt) REVERT: W 43 ASN cc_start: 0.8434 (t0) cc_final: 0.7971 (t0) REVERT: X 142 ARG cc_start: 0.8364 (mmt-90) cc_final: 0.8009 (mmt-90) REVERT: Y 112 SER cc_start: 0.7650 (p) cc_final: 0.7297 (m) REVERT: Y 123 ASN cc_start: 0.8711 (t0) cc_final: 0.8384 (t0) REVERT: Y 127 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7430 (tm-30) REVERT: Y 131 ASP cc_start: 0.7777 (m-30) cc_final: 0.7470 (m-30) REVERT: Y 144 ASN cc_start: 0.7090 (m-40) cc_final: 0.5842 (m110) REVERT: Z 117 LEU cc_start: 0.7804 (pp) cc_final: 0.7529 (mt) REVERT: Z 133 ASN cc_start: 0.9263 (t0) cc_final: 0.9028 (t0) REVERT: Z 161 LEU cc_start: 0.8602 (tp) cc_final: 0.8377 (tp) REVERT: 0 128 TYR cc_start: 0.8131 (t80) cc_final: 0.7720 (t80) REVERT: 2 127 GLN cc_start: 0.8041 (tp40) cc_final: 0.7748 (tp40) REVERT: 4 127 GLN cc_start: 0.7845 (tp40) cc_final: 0.7604 (tp-100) REVERT: 4 131 ASP cc_start: 0.8004 (p0) cc_final: 0.7638 (p0) REVERT: 4 133 ASN cc_start: 0.8014 (t0) cc_final: 0.7671 (t0) REVERT: 4 150 PHE cc_start: 0.9166 (p90) cc_final: 0.8581 (p90) REVERT: 4 151 TYR cc_start: 0.8375 (t80) cc_final: 0.8126 (t80) REVERT: 4 167 THR cc_start: 0.8761 (m) cc_final: 0.8519 (t) REVERT: 6 127 GLN cc_start: 0.8941 (tp40) cc_final: 0.8372 (tp40) REVERT: 6 138 ARG cc_start: 0.8416 (mtp85) cc_final: 0.7502 (mtm110) REVERT: 8 111 ILE cc_start: 0.9323 (mt) cc_final: 0.9092 (mt) REVERT: 8 115 ILE cc_start: 0.8928 (mt) cc_final: 0.8643 (mm) REVERT: 8 144 ASN cc_start: 0.8061 (t0) cc_final: 0.7503 (t0) REVERT: x 149 THR cc_start: 0.9372 (t) cc_final: 0.9060 (p) REVERT: x 150 PHE cc_start: 0.9327 (p90) cc_final: 0.8637 (p90) REVERT: x 153 SER cc_start: 0.9371 (t) cc_final: 0.9162 (p) REVERT: y 115 ILE cc_start: 0.9364 (mt) cc_final: 0.9161 (mt) REVERT: y 158 LEU cc_start: 0.8214 (tp) cc_final: 0.7892 (mm) REVERT: y 160 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7765 (mm-30) REVERT: y 164 ASN cc_start: 0.8605 (m-40) cc_final: 0.8320 (m-40) REVERT: z 112 SER cc_start: 0.9162 (p) cc_final: 0.8742 (m) REVERT: z 149 THR cc_start: 0.8959 (m) cc_final: 0.8596 (t) REVERT: z 151 TYR cc_start: 0.8674 (t80) cc_final: 0.8395 (t80) REVERT: 1 133 ASN cc_start: 0.8574 (m-40) cc_final: 0.8343 (t0) REVERT: 1 148 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8116 (mtpp) REVERT: 3 115 ILE cc_start: 0.8880 (mt) cc_final: 0.8336 (mt) REVERT: 5 112 SER cc_start: 0.8254 (p) cc_final: 0.8040 (m) REVERT: 5 131 ASP cc_start: 0.8198 (p0) cc_final: 0.7816 (p0) REVERT: 9 111 ILE cc_start: 0.9304 (mt) cc_final: 0.8976 (pt) REVERT: a 26 LEU cc_start: 0.8967 (tp) cc_final: 0.8690 (tp) REVERT: a 72 LYS cc_start: 0.9548 (tmtt) cc_final: 0.9274 (tptp) REVERT: b 45 GLN cc_start: 0.8492 (tp40) cc_final: 0.7660 (tm-30) REVERT: b 49 GLU cc_start: 0.7772 (mm-30) cc_final: 0.6930 (mm-30) REVERT: b 53 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8992 (mmmt) REVERT: b 59 LEU cc_start: 0.9381 (mp) cc_final: 0.9090 (mm) REVERT: b 65 SER cc_start: 0.9252 (m) cc_final: 0.8682 (t) REVERT: c 9 ASP cc_start: 0.8227 (t0) cc_final: 0.7825 (t0) REVERT: c 59 LEU cc_start: 0.9483 (mt) cc_final: 0.8959 (mt) REVERT: c 82 PHE cc_start: 0.8808 (m-10) cc_final: 0.8572 (m-10) REVERT: d 50 TYR cc_start: 0.9059 (t80) cc_final: 0.8742 (t80) REVERT: d 57 TYR cc_start: 0.9004 (t80) cc_final: 0.8451 (t80) REVERT: d 71 ILE cc_start: 0.8759 (mm) cc_final: 0.8374 (mm) REVERT: d 75 ASP cc_start: 0.8384 (m-30) cc_final: 0.8006 (m-30) REVERT: e 53 LYS cc_start: 0.9425 (mmtt) cc_final: 0.9210 (mmtp) REVERT: e 56 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8301 (tt0) REVERT: e 79 ILE cc_start: 0.9487 (tp) cc_final: 0.9199 (tt) REVERT: f 17 GLU cc_start: 0.7548 (tm-30) cc_final: 0.7113 (tm-30) REVERT: f 20 ASP cc_start: 0.8386 (t70) cc_final: 0.8175 (t0) REVERT: f 80 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8106 (tm-30) REVERT: g 14 SER cc_start: 0.8705 (m) cc_final: 0.8480 (p) REVERT: g 25 THR cc_start: 0.8152 (p) cc_final: 0.7934 (p) REVERT: g 49 GLU cc_start: 0.8416 (mp0) cc_final: 0.8200 (mp0) REVERT: g 54 LEU cc_start: 0.9232 (tp) cc_final: 0.9010 (tp) REVERT: g 79 ILE cc_start: 0.9143 (mm) cc_final: 0.8858 (mm) REVERT: h 11 THR cc_start: 0.8778 (m) cc_final: 0.8057 (m) REVERT: i 50 TYR cc_start: 0.9294 (t80) cc_final: 0.9058 (t80) REVERT: i 80 GLN cc_start: 0.8231 (tm-30) cc_final: 0.8004 (tm-30) REVERT: j 14 SER cc_start: 0.9145 (m) cc_final: 0.8317 (t) REVERT: j 80 GLN cc_start: 0.9091 (tp-100) cc_final: 0.8639 (tp-100) REVERT: k 43 ASN cc_start: 0.8154 (t0) cc_final: 0.7883 (t0) REVERT: k 50 TYR cc_start: 0.9250 (t80) cc_final: 0.9048 (t80) REVERT: l 16 SER cc_start: 0.8790 (m) cc_final: 0.8101 (t) REVERT: l 20 ASP cc_start: 0.7588 (m-30) cc_final: 0.7280 (m-30) REVERT: l 25 THR cc_start: 0.8835 (p) cc_final: 0.8187 (p) REVERT: l 26 LEU cc_start: 0.9220 (tt) cc_final: 0.8993 (tt) REVERT: l 45 GLN cc_start: 0.7981 (tp40) cc_final: 0.7500 (tp40) REVERT: l 50 TYR cc_start: 0.9190 (t80) cc_final: 0.8787 (t80) REVERT: m 20 ASP cc_start: 0.7686 (m-30) cc_final: 0.7396 (m-30) REVERT: m 24 GLN cc_start: 0.8267 (tp40) cc_final: 0.7973 (tp40) REVERT: m 43 ASN cc_start: 0.7014 (t0) cc_final: 0.6768 (t0) REVERT: m 50 TYR cc_start: 0.8740 (t80) cc_final: 0.8368 (t80) REVERT: m 75 ASP cc_start: 0.8443 (m-30) cc_final: 0.7873 (m-30) REVERT: n 3 VAL cc_start: 0.8520 (t) cc_final: 0.8172 (m) REVERT: n 14 SER cc_start: 0.9297 (t) cc_final: 0.8826 (p) REVERT: n 29 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7454 (tm-30) REVERT: n 53 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8546 (mmtm) REVERT: n 58 THR cc_start: 0.9588 (m) cc_final: 0.9365 (t) REVERT: n 75 ASP cc_start: 0.8450 (m-30) cc_final: 0.8093 (m-30) REVERT: n 80 GLN cc_start: 0.8686 (tm-30) cc_final: 0.7972 (tm-30) REVERT: o 14 SER cc_start: 0.8743 (t) cc_final: 0.8286 (p) REVERT: o 24 GLN cc_start: 0.8856 (tp40) cc_final: 0.8646 (mm110) REVERT: o 29 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7454 (mt-10) REVERT: o 37 LEU cc_start: 0.8957 (tp) cc_final: 0.8701 (tt) REVERT: o 50 TYR cc_start: 0.9292 (t80) cc_final: 0.8654 (t80) REVERT: p 12 LEU cc_start: 0.9422 (mt) cc_final: 0.9089 (mt) REVERT: p 25 THR cc_start: 0.8390 (p) cc_final: 0.7638 (t) REVERT: p 26 LEU cc_start: 0.8122 (mm) cc_final: 0.7849 (mm) REVERT: p 46 LEU cc_start: 0.9251 (tp) cc_final: 0.9042 (tt) REVERT: p 75 ASP cc_start: 0.8646 (m-30) cc_final: 0.7857 (m-30) REVERT: q 32 LEU cc_start: 0.8104 (tp) cc_final: 0.7745 (tp) REVERT: q 36 LYS cc_start: 0.8637 (mttt) cc_final: 0.8321 (mtmt) REVERT: q 67 THR cc_start: 0.9115 (m) cc_final: 0.8856 (m) REVERT: r 25 THR cc_start: 0.8182 (p) cc_final: 0.7415 (p) REVERT: r 27 GLN cc_start: 0.8854 (mt0) cc_final: 0.8507 (mt0) REVERT: r 59 LEU cc_start: 0.8801 (mt) cc_final: 0.8545 (mt) REVERT: r 80 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7913 (tm-30) REVERT: s 7 ASN cc_start: 0.6668 (m-40) cc_final: 0.5661 (p0) REVERT: s 23 THR cc_start: 0.8619 (m) cc_final: 0.8367 (m) REVERT: s 24 GLN cc_start: 0.8148 (tp40) cc_final: 0.7743 (mm-40) REVERT: s 27 GLN cc_start: 0.8492 (mt0) cc_final: 0.7920 (tm-30) REVERT: s 37 LEU cc_start: 0.9041 (tt) cc_final: 0.8809 (tp) REVERT: s 65 SER cc_start: 0.8874 (t) cc_final: 0.8592 (m) REVERT: s 69 LYS cc_start: 0.7780 (tptm) cc_final: 0.7371 (ttmt) REVERT: t 24 GLN cc_start: 0.8688 (tp40) cc_final: 0.8482 (tp40) REVERT: t 47 LEU cc_start: 0.8969 (mt) cc_final: 0.8737 (mt) REVERT: t 51 GLN cc_start: 0.8619 (tt0) cc_final: 0.6733 (mm110) REVERT: t 69 LYS cc_start: 0.9201 (tptm) cc_final: 0.8576 (mttt) REVERT: t 72 LYS cc_start: 0.9534 (tmtt) cc_final: 0.9199 (tttp) REVERT: t 75 ASP cc_start: 0.8631 (m-30) cc_final: 0.8328 (m-30) REVERT: u 30 LEU cc_start: 0.8909 (tp) cc_final: 0.8602 (tt) REVERT: u 49 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7435 (mm-30) REVERT: u 69 LYS cc_start: 0.8999 (tptm) cc_final: 0.7586 (ttmt) REVERT: u 75 ASP cc_start: 0.8950 (m-30) cc_final: 0.8188 (m-30) REVERT: v 25 THR cc_start: 0.8349 (p) cc_final: 0.8054 (p) REVERT: v 27 GLN cc_start: 0.7855 (mt0) cc_final: 0.7611 (tp40) REVERT: v 32 LEU cc_start: 0.9294 (tp) cc_final: 0.9009 (tp) REVERT: v 36 LYS cc_start: 0.9016 (mttt) cc_final: 0.8667 (mttm) REVERT: v 53 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8649 (mmmm) REVERT: v 69 LYS cc_start: 0.9093 (tptm) cc_final: 0.8168 (mttt) REVERT: w 25 THR cc_start: 0.8608 (p) cc_final: 0.8231 (p) REVERT: w 57 TYR cc_start: 0.8791 (t80) cc_final: 0.8292 (t80) REVERT: w 61 ARG cc_start: 0.8385 (mmt180) cc_final: 0.6705 (ttp-170) REVERT: a0 103 LYS cc_start: 0.8070 (tttm) cc_final: 0.7021 (tptt) REVERT: d0 103 LYS cc_start: 0.9240 (ttmt) cc_final: 0.7914 (tptt) REVERT: e0 103 LYS cc_start: 0.8747 (ttmt) cc_final: 0.7926 (tttt) REVERT: f0 103 LYS cc_start: 0.9188 (ttmt) cc_final: 0.8302 (tptt) REVERT: g0 103 LYS cc_start: 0.8974 (mtmt) cc_final: 0.7640 (tptt) REVERT: i0 103 LYS cc_start: 0.8938 (tttt) cc_final: 0.8684 (tptt) REVERT: k0 103 LYS cc_start: 0.8775 (ttmm) cc_final: 0.7650 (tptt) REVERT: l0 103 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8176 (tptt) REVERT: n0 97 SER cc_start: 0.9019 (m) cc_final: 0.8767 (t) REVERT: n0 103 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8470 (ttpt) REVERT: p0 103 LYS cc_start: 0.8856 (ttpt) cc_final: 0.8063 (tptt) REVERT: q0 103 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8266 (tptt) REVERT: r0 102 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8125 (mt-10) REVERT: r0 103 LYS cc_start: 0.8808 (ttmt) cc_final: 0.7552 (tptt) REVERT: t0 103 LYS cc_start: 0.8821 (ttmt) cc_final: 0.8096 (tptt) REVERT: t0 105 ARG cc_start: 0.9164 (ttm110) cc_final: 0.8006 (tpm170) REVERT: u0 100 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7468 (tpt170) REVERT: u0 103 LYS cc_start: 0.9081 (ttmt) cc_final: 0.8065 (tptt) REVERT: v0 92 THR cc_start: 0.8397 (m) cc_final: 0.8119 (m) REVERT: v0 103 LYS cc_start: 0.9280 (mttt) cc_final: 0.7826 (tptt) REVERT: w0 103 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8403 (tptt) REVERT: x0 103 LYS cc_start: 0.8420 (ttmt) cc_final: 0.7726 (tptt) outliers start: 7 outliers final: 0 residues processed: 2240 average time/residue: 0.5340 time to fit residues: 2021.1378 Evaluate side-chains 1926 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1926 time to evaluate : 5.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 421 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 376 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 431 optimal weight: 0.9980 chunk 349 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 453 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 HIS D 131 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 247 HIS F 252 ASN I 9 ASN K 162 GLN N 8 ASN O 44 GLN P 59 ASN R 19 GLN T 80 GLN U 80 GLN ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 123 ASN ** 3 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 164 ASN 9 123 ASN b 43 ASN b 64 GLN ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN d 24 GLN ** f 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** m 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 64 GLN p 80 GLN r 24 GLN u 40 ASN v 81 ASN w 64 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 44858 Z= 0.231 Angle : 0.617 9.747 60890 Z= 0.306 Chirality : 0.040 0.201 7369 Planarity : 0.004 0.066 7620 Dihedral : 4.185 88.245 5953 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.20 % Allowed : 1.86 % Favored : 97.94 % 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: 3.04 (0.12), residues: 5404 helix: 3.12 (0.08), residues: 4153 sheet: 1.22 (0.33), residues: 224 loop : -2.94 (0.17), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 66 HIS 0.007 0.001 HIS B 106 PHE 0.041 0.002 PHE r 19 TYR 0.032 0.001 TYR K 171 ARG 0.009 0.000 ARG K 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2211 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 2201 time to evaluate : 5.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8503 (p) cc_final: 0.7753 (p) REVERT: A 36 MET cc_start: 0.8794 (ttp) cc_final: 0.8360 (ttm) REVERT: A 48 SER cc_start: 0.9099 (m) cc_final: 0.8886 (m) REVERT: A 50 MET cc_start: 0.8245 (ttp) cc_final: 0.8016 (ttm) REVERT: A 68 ILE cc_start: 0.9542 (mt) cc_final: 0.9218 (mt) REVERT: A 69 GLU cc_start: 0.7755 (tp30) cc_final: 0.7256 (mm-30) REVERT: A 101 GLN cc_start: 0.8896 (tt0) cc_final: 0.8405 (tm-30) REVERT: A 142 TYR cc_start: 0.9202 (t80) cc_final: 0.8796 (t80) REVERT: A 152 LYS cc_start: 0.9191 (tttt) cc_final: 0.8667 (mtmt) REVERT: A 177 MET cc_start: 0.8035 (mtt) cc_final: 0.7707 (mtp) REVERT: A 205 LYS cc_start: 0.9032 (mttt) cc_final: 0.8055 (tttt) REVERT: B 65 LYS cc_start: 0.8645 (tttp) cc_final: 0.8232 (tmtt) REVERT: B 110 GLU cc_start: 0.8748 (pm20) cc_final: 0.8450 (pm20) REVERT: B 146 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 177 MET cc_start: 0.8175 (mtt) cc_final: 0.7847 (mtt) REVERT: B 190 LYS cc_start: 0.9203 (mtmt) cc_final: 0.8098 (mtmm) REVERT: C 25 THR cc_start: 0.9315 (p) cc_final: 0.8801 (t) REVERT: C 59 MET cc_start: 0.8731 (mtp) cc_final: 0.8506 (mtp) REVERT: C 117 ARG cc_start: 0.8459 (mtt180) cc_final: 0.7974 (tpt170) REVERT: C 146 GLU cc_start: 0.8572 (tp30) cc_final: 0.8250 (mm-30) REVERT: C 177 MET cc_start: 0.7399 (ptp) cc_final: 0.7016 (mtt) REVERT: C 211 TYR cc_start: 0.8156 (m-80) cc_final: 0.7584 (m-80) REVERT: D 2 LEU cc_start: 0.9225 (mt) cc_final: 0.8978 (mt) REVERT: D 6 SER cc_start: 0.8837 (m) cc_final: 0.8163 (p) REVERT: D 17 LEU cc_start: 0.9261 (tp) cc_final: 0.8854 (tt) REVERT: D 156 TYR cc_start: 0.8676 (m-10) cc_final: 0.8143 (m-10) REVERT: E 44 GLN cc_start: 0.8479 (mm-40) cc_final: 0.8226 (mp10) REVERT: E 64 MET cc_start: 0.8684 (mmm) cc_final: 0.7618 (mmm) REVERT: E 162 VAL cc_start: 0.9376 (t) cc_final: 0.9139 (p) REVERT: F 133 PHE cc_start: 0.8904 (t80) cc_final: 0.8486 (t80) REVERT: F 152 GLN cc_start: 0.9081 (tt0) cc_final: 0.8462 (tp-100) REVERT: F 170 ASN cc_start: 0.8458 (m110) cc_final: 0.8257 (m-40) REVERT: F 202 VAL cc_start: 0.9058 (t) cc_final: 0.8791 (t) REVERT: G 52 LYS cc_start: 0.8893 (mtmt) cc_final: 0.8549 (mtmt) REVERT: G 79 MET cc_start: 0.8708 (mmm) cc_final: 0.8175 (mmm) REVERT: H 79 MET cc_start: 0.8119 (mmp) cc_final: 0.7482 (mmp) REVERT: I 5 VAL cc_start: 0.9074 (t) cc_final: 0.8503 (p) REVERT: I 53 LEU cc_start: 0.7994 (tp) cc_final: 0.7649 (tp) REVERT: I 60 LEU cc_start: 0.8558 (mt) cc_final: 0.8323 (mt) REVERT: K 32 VAL cc_start: 0.6993 (t) cc_final: 0.6702 (t) REVERT: K 51 MET cc_start: 0.7809 (mmt) cc_final: 0.7539 (mmt) REVERT: K 132 LYS cc_start: 0.8613 (mmtp) cc_final: 0.8197 (mttt) REVERT: N 58 LEU cc_start: 0.9213 (mt) cc_final: 0.8865 (mt) REVERT: N 68 THR cc_start: 0.8905 (m) cc_final: 0.8596 (t) REVERT: O 41 THR cc_start: 0.8679 (t) cc_final: 0.8352 (m) REVERT: P 44 GLN cc_start: 0.8264 (tt0) cc_final: 0.7957 (tt0) REVERT: P 46 SER cc_start: 0.9526 (m) cc_final: 0.9143 (t) REVERT: P 56 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7165 (tm-30) REVERT: P 57 SER cc_start: 0.9065 (m) cc_final: 0.8427 (p) REVERT: R 27 GLU cc_start: 0.7335 (tm-30) cc_final: 0.7020 (pt0) REVERT: S 37 LEU cc_start: 0.9085 (tp) cc_final: 0.8726 (tp) REVERT: T 30 LEU cc_start: 0.9173 (tp) cc_final: 0.8912 (tp) REVERT: T 50 TYR cc_start: 0.9071 (t80) cc_final: 0.8831 (t80) REVERT: U 81 ASN cc_start: 0.9141 (m-40) cc_final: 0.8719 (m-40) REVERT: V 32 LEU cc_start: 0.8705 (mt) cc_final: 0.8331 (tt) REVERT: V 64 GLN cc_start: 0.8608 (tt0) cc_final: 0.8333 (tt0) REVERT: W 39 LYS cc_start: 0.8354 (mttt) cc_final: 0.7759 (mptt) REVERT: W 43 ASN cc_start: 0.8626 (t0) cc_final: 0.8014 (t0) REVERT: X 142 ARG cc_start: 0.8418 (mmt-90) cc_final: 0.8083 (mmt-90) REVERT: Y 112 SER cc_start: 0.7899 (p) cc_final: 0.7643 (m) REVERT: Y 123 ASN cc_start: 0.8737 (t0) cc_final: 0.8430 (t0) REVERT: Y 127 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7451 (tm-30) REVERT: Y 131 ASP cc_start: 0.7818 (m-30) cc_final: 0.7458 (m-30) REVERT: Z 133 ASN cc_start: 0.9251 (t0) cc_final: 0.9038 (t0) REVERT: Z 161 LEU cc_start: 0.8617 (tp) cc_final: 0.8384 (tp) REVERT: 0 128 TYR cc_start: 0.8192 (t80) cc_final: 0.7752 (t80) REVERT: 2 127 GLN cc_start: 0.8217 (tp40) cc_final: 0.7871 (tp40) REVERT: 4 127 GLN cc_start: 0.7875 (tp40) cc_final: 0.7652 (tp-100) REVERT: 4 131 ASP cc_start: 0.8111 (p0) cc_final: 0.7800 (p0) REVERT: 4 150 PHE cc_start: 0.9150 (p90) cc_final: 0.8559 (p90) REVERT: 4 151 TYR cc_start: 0.8452 (t80) cc_final: 0.8136 (t80) REVERT: 4 167 THR cc_start: 0.8745 (m) cc_final: 0.8490 (t) REVERT: 6 127 GLN cc_start: 0.8951 (tp40) cc_final: 0.8381 (tp40) REVERT: 6 138 ARG cc_start: 0.8414 (mtp85) cc_final: 0.7663 (mtm110) REVERT: 6 149 THR cc_start: 0.9042 (m) cc_final: 0.8235 (p) REVERT: 8 115 ILE cc_start: 0.8908 (mt) cc_final: 0.8643 (mm) REVERT: 8 144 ASN cc_start: 0.7978 (t0) cc_final: 0.7504 (t0) REVERT: x 149 THR cc_start: 0.9420 (t) cc_final: 0.9148 (p) REVERT: x 150 PHE cc_start: 0.9340 (p90) cc_final: 0.8771 (p90) REVERT: x 153 SER cc_start: 0.9547 (t) cc_final: 0.9007 (p) REVERT: x 168 LEU cc_start: 0.9419 (tp) cc_final: 0.9117 (tt) REVERT: y 115 ILE cc_start: 0.9429 (mt) cc_final: 0.9218 (mt) REVERT: y 158 LEU cc_start: 0.8240 (tp) cc_final: 0.7891 (mm) REVERT: y 160 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7789 (mm-30) REVERT: z 112 SER cc_start: 0.9163 (p) cc_final: 0.8871 (m) REVERT: z 127 GLN cc_start: 0.8426 (tm-30) cc_final: 0.7991 (tm-30) REVERT: z 138 ARG cc_start: 0.8269 (ttp-170) cc_final: 0.8038 (ttp-110) REVERT: z 149 THR cc_start: 0.9041 (m) cc_final: 0.8624 (t) REVERT: 1 130 LYS cc_start: 0.8396 (mmmt) cc_final: 0.8089 (mmtt) REVERT: 1 133 ASN cc_start: 0.8655 (m-40) cc_final: 0.8310 (t0) REVERT: 1 148 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8134 (mtpp) REVERT: 3 115 ILE cc_start: 0.8902 (mt) cc_final: 0.8363 (mt) REVERT: 3 118 GLU cc_start: 0.6277 (tp30) cc_final: 0.6050 (tp30) REVERT: 5 131 ASP cc_start: 0.8216 (p0) cc_final: 0.7751 (p0) REVERT: 7 168 LEU cc_start: 0.9113 (tp) cc_final: 0.8896 (tp) REVERT: 9 128 TYR cc_start: 0.8776 (t80) cc_final: 0.8504 (t80) REVERT: a 26 LEU cc_start: 0.8947 (tp) cc_final: 0.8619 (tp) REVERT: a 31 THR cc_start: 0.7964 (m) cc_final: 0.7537 (m) REVERT: a 72 LYS cc_start: 0.9583 (tmtt) cc_final: 0.9150 (tptp) REVERT: b 14 SER cc_start: 0.8890 (m) cc_final: 0.8651 (p) REVERT: b 45 GLN cc_start: 0.8551 (tp40) cc_final: 0.7730 (tm-30) REVERT: b 49 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6941 (mm-30) REVERT: b 59 LEU cc_start: 0.9354 (mp) cc_final: 0.9099 (mp) REVERT: b 65 SER cc_start: 0.9237 (m) cc_final: 0.8844 (t) REVERT: c 9 ASP cc_start: 0.8371 (t0) cc_final: 0.7968 (t0) REVERT: c 59 LEU cc_start: 0.9458 (mt) cc_final: 0.8946 (mt) REVERT: c 82 PHE cc_start: 0.8787 (m-10) cc_final: 0.8586 (m-10) REVERT: d 4 THR cc_start: 0.9004 (m) cc_final: 0.8537 (p) REVERT: d 43 ASN cc_start: 0.8553 (t0) cc_final: 0.8236 (t0) REVERT: d 50 TYR cc_start: 0.9104 (t80) cc_final: 0.8746 (t80) REVERT: d 57 TYR cc_start: 0.9000 (t80) cc_final: 0.8478 (t80) REVERT: d 75 ASP cc_start: 0.8354 (m-30) cc_final: 0.8009 (m-30) REVERT: e 42 SER cc_start: 0.9407 (m) cc_final: 0.9102 (t) REVERT: e 56 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8342 (tt0) REVERT: e 79 ILE cc_start: 0.9336 (tp) cc_final: 0.9071 (tt) REVERT: f 17 GLU cc_start: 0.7556 (tm-30) cc_final: 0.6980 (tm-30) REVERT: f 37 LEU cc_start: 0.8553 (tt) cc_final: 0.8269 (tt) REVERT: f 80 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8007 (tm-30) REVERT: g 25 THR cc_start: 0.8151 (p) cc_final: 0.7947 (p) REVERT: g 54 LEU cc_start: 0.9299 (tp) cc_final: 0.9007 (tp) REVERT: g 79 ILE cc_start: 0.9155 (mm) cc_final: 0.8708 (mm) REVERT: h 19 PHE cc_start: 0.7305 (t80) cc_final: 0.6932 (t80) REVERT: h 59 LEU cc_start: 0.9154 (mp) cc_final: 0.8815 (mp) REVERT: j 14 SER cc_start: 0.9198 (m) cc_final: 0.8428 (t) REVERT: j 80 GLN cc_start: 0.9182 (tp-100) cc_final: 0.8867 (tp-100) REVERT: k 37 LEU cc_start: 0.8994 (tp) cc_final: 0.8636 (tt) REVERT: k 50 TYR cc_start: 0.9282 (t80) cc_final: 0.8888 (t80) REVERT: l 16 SER cc_start: 0.8917 (m) cc_final: 0.8150 (t) REVERT: l 25 THR cc_start: 0.8659 (p) cc_final: 0.7992 (p) REVERT: l 45 GLN cc_start: 0.8045 (tp40) cc_final: 0.7521 (tp40) REVERT: l 50 TYR cc_start: 0.9217 (t80) cc_final: 0.8798 (t80) REVERT: m 20 ASP cc_start: 0.7816 (m-30) cc_final: 0.7432 (m-30) REVERT: m 24 GLN cc_start: 0.8499 (tp40) cc_final: 0.8014 (tp40) REVERT: m 50 TYR cc_start: 0.8793 (t80) cc_final: 0.8478 (t80) REVERT: m 75 ASP cc_start: 0.8448 (m-30) cc_final: 0.7915 (m-30) REVERT: n 3 VAL cc_start: 0.8538 (t) cc_final: 0.8240 (m) REVERT: n 29 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7417 (tm-30) REVERT: n 53 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8495 (mmtm) REVERT: n 75 ASP cc_start: 0.8498 (m-30) cc_final: 0.8094 (m-30) REVERT: n 80 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8036 (tm-30) REVERT: o 14 SER cc_start: 0.8772 (t) cc_final: 0.8424 (p) REVERT: o 29 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7547 (mt-10) REVERT: o 37 LEU cc_start: 0.9003 (tp) cc_final: 0.8756 (tt) REVERT: o 50 TYR cc_start: 0.9356 (t80) cc_final: 0.8679 (t80) REVERT: o 75 ASP cc_start: 0.7572 (t0) cc_final: 0.7357 (t0) REVERT: p 12 LEU cc_start: 0.9449 (mt) cc_final: 0.9133 (mt) REVERT: p 25 THR cc_start: 0.8396 (p) cc_final: 0.7634 (t) REVERT: p 26 LEU cc_start: 0.8132 (mm) cc_final: 0.7849 (mm) REVERT: p 75 ASP cc_start: 0.8662 (m-30) cc_final: 0.7937 (m-30) REVERT: q 32 LEU cc_start: 0.8258 (tp) cc_final: 0.7871 (tp) REVERT: q 36 LYS cc_start: 0.8685 (mttt) cc_final: 0.8422 (mtmt) REVERT: r 25 THR cc_start: 0.8232 (p) cc_final: 0.7641 (p) REVERT: r 29 GLU cc_start: 0.8937 (pm20) cc_final: 0.8457 (pm20) REVERT: r 59 LEU cc_start: 0.8881 (mt) cc_final: 0.8569 (mt) REVERT: r 80 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8021 (tm-30) REVERT: s 7 ASN cc_start: 0.6603 (m-40) cc_final: 0.5521 (p0) REVERT: s 23 THR cc_start: 0.8675 (m) cc_final: 0.8343 (m) REVERT: s 27 GLN cc_start: 0.8509 (mt0) cc_final: 0.7732 (tm-30) REVERT: s 65 SER cc_start: 0.9049 (t) cc_final: 0.8704 (m) REVERT: s 69 LYS cc_start: 0.8535 (tptm) cc_final: 0.7391 (ttmt) REVERT: t 24 GLN cc_start: 0.8663 (tp40) cc_final: 0.8390 (tp40) REVERT: t 56 GLU cc_start: 0.8284 (tp30) cc_final: 0.8081 (tp30) REVERT: t 69 LYS cc_start: 0.9245 (tptm) cc_final: 0.8567 (mttt) REVERT: t 72 LYS cc_start: 0.9529 (tmtt) cc_final: 0.9202 (tttp) REVERT: u 30 LEU cc_start: 0.8838 (tp) cc_final: 0.8591 (tt) REVERT: u 49 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7451 (tp30) REVERT: u 69 LYS cc_start: 0.8959 (tptm) cc_final: 0.7506 (ttmt) REVERT: u 75 ASP cc_start: 0.8934 (m-30) cc_final: 0.8185 (m-30) REVERT: v 25 THR cc_start: 0.8495 (p) cc_final: 0.8173 (p) REVERT: v 27 GLN cc_start: 0.8055 (mt0) cc_final: 0.7666 (tp40) REVERT: v 32 LEU cc_start: 0.9313 (tp) cc_final: 0.9041 (tp) REVERT: v 36 LYS cc_start: 0.9055 (mttt) cc_final: 0.8773 (mttp) REVERT: v 53 LYS cc_start: 0.8911 (mmmt) cc_final: 0.8672 (mmmm) REVERT: v 69 LYS cc_start: 0.9112 (tptm) cc_final: 0.8246 (mttt) REVERT: w 25 THR cc_start: 0.8616 (p) cc_final: 0.8247 (p) REVERT: w 57 TYR cc_start: 0.8886 (t80) cc_final: 0.8388 (t80) REVERT: w 61 ARG cc_start: 0.8380 (mmt180) cc_final: 0.6669 (ttp-170) REVERT: w 69 LYS cc_start: 0.9030 (tppt) cc_final: 0.8789 (tppt) REVERT: a0 103 LYS cc_start: 0.8160 (tttm) cc_final: 0.7095 (tptt) REVERT: d0 103 LYS cc_start: 0.9264 (ttmt) cc_final: 0.7926 (tptt) REVERT: e0 103 LYS cc_start: 0.8751 (ttmt) cc_final: 0.7983 (tttt) REVERT: f0 103 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8314 (tptt) REVERT: g0 103 LYS cc_start: 0.9042 (mtmt) cc_final: 0.7660 (tptt) REVERT: i0 103 LYS cc_start: 0.8981 (tttt) cc_final: 0.8651 (tptt) REVERT: k0 103 LYS cc_start: 0.8842 (ttmm) cc_final: 0.7700 (tptt) REVERT: l0 103 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8182 (tptt) REVERT: m0 103 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8205 (tptt) REVERT: n0 97 SER cc_start: 0.9115 (m) cc_final: 0.8834 (t) REVERT: p0 103 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8090 (tptt) REVERT: q0 103 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8316 (tptt) REVERT: r0 102 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8134 (mt-10) REVERT: r0 103 LYS cc_start: 0.8842 (ttmt) cc_final: 0.7559 (tptt) REVERT: t0 103 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8145 (tptt) REVERT: t0 105 ARG cc_start: 0.9206 (ttm110) cc_final: 0.8041 (tpm170) REVERT: u0 100 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7516 (tpt170) REVERT: u0 103 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8079 (tptt) REVERT: v0 92 THR cc_start: 0.8583 (m) cc_final: 0.8308 (m) REVERT: v0 103 LYS cc_start: 0.9275 (mttt) cc_final: 0.7902 (tptt) REVERT: w0 103 LYS cc_start: 0.8882 (ttmt) cc_final: 0.8399 (tptt) REVERT: x0 103 LYS cc_start: 0.8500 (ttmt) cc_final: 0.7914 (tptt) outliers start: 10 outliers final: 1 residues processed: 2204 average time/residue: 0.5048 time to fit residues: 1871.1378 Evaluate side-chains 1914 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1913 time to evaluate : 5.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 170 optimal weight: 4.9990 chunk 455 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 296 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 506 optimal weight: 1.9990 chunk 420 optimal weight: 0.5980 chunk 234 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 167 optimal weight: 0.6980 chunk 265 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** E 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 106 HIS ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 247 HIS F 252 ASN J 76 HIS O 9 GLN O 44 GLN P 59 ASN R 19 GLN T 80 GLN Y 144 ASN ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 137 HIS ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 133 ASN ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 164 ASN 7 123 ASN ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 123 ASN ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN m 27 GLN ** r 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 40 ASN v 81 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 44858 Z= 0.195 Angle : 0.610 10.378 60890 Z= 0.301 Chirality : 0.039 0.198 7369 Planarity : 0.004 0.069 7620 Dihedral : 4.197 89.659 5953 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.12 % Allowed : 1.76 % Favored : 98.12 % 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: 3.04 (0.12), residues: 5404 helix: 3.12 (0.08), residues: 4150 sheet: 1.24 (0.33), residues: 224 loop : -2.94 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 66 HIS 0.006 0.001 HIS F 11 PHE 0.034 0.002 PHE j 19 TYR 0.025 0.001 TYR O 3 ARG 0.006 0.000 ARG K 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2223 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2217 time to evaluate : 5.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8601 (p) cc_final: 0.7685 (p) REVERT: A 36 MET cc_start: 0.8825 (ttp) cc_final: 0.8386 (tpp) REVERT: A 50 MET cc_start: 0.8144 (ttp) cc_final: 0.7841 (ttm) REVERT: A 68 ILE cc_start: 0.9459 (mt) cc_final: 0.9232 (mt) REVERT: A 69 GLU cc_start: 0.7776 (tp30) cc_final: 0.7178 (mm-30) REVERT: A 97 MET cc_start: 0.8037 (tpt) cc_final: 0.7758 (tpt) REVERT: A 101 GLN cc_start: 0.8921 (tt0) cc_final: 0.8378 (tm-30) REVERT: A 142 TYR cc_start: 0.9118 (t80) cc_final: 0.8524 (t80) REVERT: A 152 LYS cc_start: 0.9149 (tttt) cc_final: 0.8711 (mtmt) REVERT: A 205 LYS cc_start: 0.9050 (mttt) cc_final: 0.8021 (tttt) REVERT: B 65 LYS cc_start: 0.8590 (tttp) cc_final: 0.8131 (tmtt) REVERT: B 110 GLU cc_start: 0.8718 (pm20) cc_final: 0.8437 (pm20) REVERT: B 116 GLN cc_start: 0.8716 (tp40) cc_final: 0.8485 (tp40) REVERT: B 177 MET cc_start: 0.8104 (mtt) cc_final: 0.7764 (mtt) REVERT: B 190 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8075 (mtmm) REVERT: C 25 THR cc_start: 0.9280 (p) cc_final: 0.8817 (t) REVERT: C 72 TYR cc_start: 0.5589 (t80) cc_final: 0.5269 (m-10) REVERT: C 104 LYS cc_start: 0.8430 (mtmm) cc_final: 0.8199 (mtmt) REVERT: C 117 ARG cc_start: 0.8430 (mtt180) cc_final: 0.7963 (tpt170) REVERT: C 146 GLU cc_start: 0.8541 (tp30) cc_final: 0.8224 (mm-30) REVERT: C 180 MET cc_start: 0.8118 (tpp) cc_final: 0.7638 (tpp) REVERT: D 2 LEU cc_start: 0.9210 (mt) cc_final: 0.8977 (mt) REVERT: D 6 SER cc_start: 0.8783 (m) cc_final: 0.8118 (p) REVERT: D 29 LYS cc_start: 0.8830 (tptt) cc_final: 0.8604 (tptt) REVERT: D 101 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8056 (mm-40) REVERT: D 156 TYR cc_start: 0.8604 (m-10) cc_final: 0.8092 (m-10) REVERT: E 64 MET cc_start: 0.8703 (mmm) cc_final: 0.8039 (mmm) REVERT: E 106 HIS cc_start: 0.8221 (m-70) cc_final: 0.7993 (m90) REVERT: F 104 ASP cc_start: 0.8379 (t0) cc_final: 0.8154 (t0) REVERT: F 110 THR cc_start: 0.7966 (t) cc_final: 0.7757 (t) REVERT: F 133 PHE cc_start: 0.8868 (t80) cc_final: 0.8475 (t80) REVERT: F 139 LEU cc_start: 0.9232 (tp) cc_final: 0.9006 (tp) REVERT: F 152 GLN cc_start: 0.9053 (tt0) cc_final: 0.8463 (tp-100) REVERT: F 170 ASN cc_start: 0.8405 (m110) cc_final: 0.8179 (m-40) REVERT: G 52 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8536 (mtmt) REVERT: G 79 MET cc_start: 0.8692 (mmm) cc_final: 0.8151 (mmm) REVERT: H 77 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7777 (tm-30) REVERT: H 79 MET cc_start: 0.8085 (mmp) cc_final: 0.7439 (mmp) REVERT: I 5 VAL cc_start: 0.9156 (t) cc_final: 0.8559 (p) REVERT: I 60 LEU cc_start: 0.8548 (mt) cc_final: 0.8310 (mt) REVERT: I 69 GLU cc_start: 0.7589 (tp30) cc_final: 0.6485 (tp30) REVERT: K 51 MET cc_start: 0.7735 (mmt) cc_final: 0.7528 (mmt) REVERT: K 132 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8184 (mttt) REVERT: N 58 LEU cc_start: 0.9189 (mt) cc_final: 0.8869 (mt) REVERT: O 41 THR cc_start: 0.8823 (t) cc_final: 0.8463 (m) REVERT: P 44 GLN cc_start: 0.8312 (tt0) cc_final: 0.7891 (tt0) REVERT: P 46 SER cc_start: 0.9463 (m) cc_final: 0.9144 (t) REVERT: P 56 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7124 (tm-30) REVERT: P 57 SER cc_start: 0.9165 (m) cc_final: 0.8474 (p) REVERT: R 27 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6925 (pt0) REVERT: S 25 THR cc_start: 0.7731 (t) cc_final: 0.7365 (t) REVERT: S 37 LEU cc_start: 0.9093 (tp) cc_final: 0.8695 (tp) REVERT: T 30 LEU cc_start: 0.9156 (tp) cc_final: 0.8874 (tp) REVERT: T 50 TYR cc_start: 0.9039 (t80) cc_final: 0.8793 (t80) REVERT: U 81 ASN cc_start: 0.9153 (m-40) cc_final: 0.8739 (m-40) REVERT: V 32 LEU cc_start: 0.8673 (mt) cc_final: 0.8316 (tt) REVERT: V 64 GLN cc_start: 0.8564 (tt0) cc_final: 0.8289 (tt0) REVERT: W 39 LYS cc_start: 0.8167 (mttt) cc_final: 0.7604 (mptt) REVERT: W 43 ASN cc_start: 0.8573 (t0) cc_final: 0.7932 (t0) REVERT: X 142 ARG cc_start: 0.8599 (mmt-90) cc_final: 0.8189 (mmt-90) REVERT: Y 112 SER cc_start: 0.7917 (p) cc_final: 0.7613 (m) REVERT: Y 123 ASN cc_start: 0.8691 (t0) cc_final: 0.8412 (t0) REVERT: Y 127 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7586 (tm-30) REVERT: Y 131 ASP cc_start: 0.7822 (m-30) cc_final: 0.7417 (m-30) REVERT: Z 133 ASN cc_start: 0.9188 (t0) cc_final: 0.8962 (t0) REVERT: Z 158 LEU cc_start: 0.9002 (tt) cc_final: 0.8681 (mm) REVERT: Z 161 LEU cc_start: 0.8595 (tp) cc_final: 0.8364 (tp) REVERT: 0 128 TYR cc_start: 0.8050 (t80) cc_final: 0.7691 (t80) REVERT: 0 161 LEU cc_start: 0.9063 (tp) cc_final: 0.8575 (tp) REVERT: 2 127 GLN cc_start: 0.8237 (tp40) cc_final: 0.7926 (tp40) REVERT: 4 131 ASP cc_start: 0.8107 (p0) cc_final: 0.7773 (p0) REVERT: 4 150 PHE cc_start: 0.9110 (p90) cc_final: 0.8597 (p90) REVERT: 4 167 THR cc_start: 0.8690 (m) cc_final: 0.8452 (t) REVERT: 6 127 GLN cc_start: 0.8904 (tp40) cc_final: 0.8249 (tp40) REVERT: 6 149 THR cc_start: 0.9033 (m) cc_final: 0.8198 (p) REVERT: 8 111 ILE cc_start: 0.9292 (mt) cc_final: 0.9069 (mt) REVERT: 8 115 ILE cc_start: 0.8901 (mt) cc_final: 0.8645 (mm) REVERT: 8 144 ASN cc_start: 0.7878 (t0) cc_final: 0.7474 (t0) REVERT: x 149 THR cc_start: 0.9426 (t) cc_final: 0.9124 (p) REVERT: x 150 PHE cc_start: 0.9263 (p90) cc_final: 0.8655 (p90) REVERT: x 153 SER cc_start: 0.9556 (t) cc_final: 0.9042 (p) REVERT: x 168 LEU cc_start: 0.9347 (tp) cc_final: 0.9099 (tt) REVERT: y 115 ILE cc_start: 0.9352 (mt) cc_final: 0.9138 (mt) REVERT: y 144 ASN cc_start: 0.8154 (t0) cc_final: 0.7947 (t0) REVERT: y 158 LEU cc_start: 0.8260 (tp) cc_final: 0.7888 (mm) REVERT: y 160 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7786 (mm-30) REVERT: y 164 ASN cc_start: 0.8651 (m-40) cc_final: 0.8374 (m-40) REVERT: z 112 SER cc_start: 0.9174 (p) cc_final: 0.8743 (m) REVERT: z 127 GLN cc_start: 0.8419 (tm-30) cc_final: 0.7973 (tm-30) REVERT: z 149 THR cc_start: 0.9002 (m) cc_final: 0.8577 (t) REVERT: z 151 TYR cc_start: 0.8751 (t80) cc_final: 0.8274 (t80) REVERT: 1 127 GLN cc_start: 0.8001 (tp40) cc_final: 0.7640 (tp40) REVERT: 1 130 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8159 (mmtt) REVERT: 1 133 ASN cc_start: 0.8647 (m-40) cc_final: 0.8347 (t0) REVERT: 1 148 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8171 (mtpp) REVERT: 3 115 ILE cc_start: 0.8867 (mt) cc_final: 0.8318 (mt) REVERT: 3 118 GLU cc_start: 0.6247 (tp30) cc_final: 0.6034 (tp30) REVERT: 5 131 ASP cc_start: 0.8173 (p0) cc_final: 0.7757 (p0) REVERT: 9 128 TYR cc_start: 0.8786 (t80) cc_final: 0.8510 (t80) REVERT: a 26 LEU cc_start: 0.8896 (tp) cc_final: 0.8594 (tp) REVERT: a 31 THR cc_start: 0.8043 (m) cc_final: 0.7695 (m) REVERT: a 72 LYS cc_start: 0.9546 (tmtt) cc_final: 0.9143 (tptp) REVERT: a 80 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8382 (tm-30) REVERT: b 14 SER cc_start: 0.8900 (m) cc_final: 0.8613 (p) REVERT: b 45 GLN cc_start: 0.8557 (tp40) cc_final: 0.7668 (tm-30) REVERT: b 49 GLU cc_start: 0.7634 (mm-30) cc_final: 0.6907 (mm-30) REVERT: b 59 LEU cc_start: 0.9298 (mp) cc_final: 0.9061 (mp) REVERT: b 65 SER cc_start: 0.9226 (m) cc_final: 0.8706 (t) REVERT: c 59 LEU cc_start: 0.9454 (mt) cc_final: 0.8951 (mt) REVERT: c 82 PHE cc_start: 0.8767 (m-10) cc_final: 0.8541 (m-10) REVERT: d 4 THR cc_start: 0.8954 (m) cc_final: 0.8475 (p) REVERT: d 50 TYR cc_start: 0.9091 (t80) cc_final: 0.8740 (t80) REVERT: d 54 LEU cc_start: 0.9159 (tp) cc_final: 0.8952 (tp) REVERT: d 57 TYR cc_start: 0.9027 (t80) cc_final: 0.8451 (t80) REVERT: d 71 ILE cc_start: 0.8709 (mm) cc_final: 0.8206 (mm) REVERT: d 75 ASP cc_start: 0.8287 (m-30) cc_final: 0.7962 (m-30) REVERT: e 42 SER cc_start: 0.9372 (m) cc_final: 0.9059 (t) REVERT: e 56 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8245 (tt0) REVERT: e 79 ILE cc_start: 0.9365 (tp) cc_final: 0.9156 (tt) REVERT: f 37 LEU cc_start: 0.8604 (tt) cc_final: 0.8282 (tt) REVERT: f 80 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7938 (tm-30) REVERT: g 79 ILE cc_start: 0.9186 (mm) cc_final: 0.8931 (mm) REVERT: h 11 THR cc_start: 0.8859 (m) cc_final: 0.8291 (m) REVERT: h 59 LEU cc_start: 0.9046 (mp) cc_final: 0.8603 (mp) REVERT: h 60 TYR cc_start: 0.7866 (t80) cc_final: 0.7601 (t80) REVERT: i 80 GLN cc_start: 0.8337 (tm-30) cc_final: 0.7995 (tm-30) REVERT: j 14 SER cc_start: 0.9156 (m) cc_final: 0.8595 (t) REVERT: j 80 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8842 (tp-100) REVERT: k 37 LEU cc_start: 0.8958 (tp) cc_final: 0.8622 (tt) REVERT: k 50 TYR cc_start: 0.9287 (t80) cc_final: 0.8884 (t80) REVERT: k 80 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8147 (tp40) REVERT: l 16 SER cc_start: 0.8980 (m) cc_final: 0.8169 (t) REVERT: l 20 ASP cc_start: 0.7504 (m-30) cc_final: 0.7281 (m-30) REVERT: l 25 THR cc_start: 0.8737 (p) cc_final: 0.7961 (p) REVERT: l 26 LEU cc_start: 0.9167 (tt) cc_final: 0.8966 (tt) REVERT: l 45 GLN cc_start: 0.8003 (tp40) cc_final: 0.7548 (tp40) REVERT: l 50 TYR cc_start: 0.9188 (t80) cc_final: 0.8761 (t80) REVERT: m 20 ASP cc_start: 0.7835 (m-30) cc_final: 0.7407 (m-30) REVERT: m 24 GLN cc_start: 0.8868 (tp40) cc_final: 0.8559 (tp40) REVERT: m 27 GLN cc_start: 0.7991 (pt0) cc_final: 0.7430 (pt0) REVERT: m 50 TYR cc_start: 0.8773 (t80) cc_final: 0.8377 (t80) REVERT: m 75 ASP cc_start: 0.8432 (m-30) cc_final: 0.7869 (m-30) REVERT: n 3 VAL cc_start: 0.8535 (t) cc_final: 0.8245 (m) REVERT: n 29 GLU cc_start: 0.7892 (tm-30) cc_final: 0.7204 (tm-30) REVERT: n 49 GLU cc_start: 0.7102 (tm-30) cc_final: 0.6791 (tm-30) REVERT: n 53 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8426 (mmtm) REVERT: n 75 ASP cc_start: 0.8450 (m-30) cc_final: 0.8104 (m-30) REVERT: n 80 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8008 (tm-30) REVERT: o 14 SER cc_start: 0.8812 (t) cc_final: 0.8412 (p) REVERT: o 29 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7543 (mt-10) REVERT: o 43 ASN cc_start: 0.7190 (t0) cc_final: 0.6868 (t0) REVERT: o 50 TYR cc_start: 0.9319 (t80) cc_final: 0.8690 (t80) REVERT: p 12 LEU cc_start: 0.9450 (mt) cc_final: 0.9167 (mt) REVERT: p 25 THR cc_start: 0.8359 (p) cc_final: 0.7612 (t) REVERT: p 26 LEU cc_start: 0.8131 (mm) cc_final: 0.7878 (mm) REVERT: p 75 ASP cc_start: 0.8637 (m-30) cc_final: 0.7920 (m-30) REVERT: q 32 LEU cc_start: 0.8160 (tp) cc_final: 0.7776 (tp) REVERT: q 36 LYS cc_start: 0.8663 (mttt) cc_final: 0.8414 (mtmt) REVERT: r 25 THR cc_start: 0.8290 (p) cc_final: 0.7569 (p) REVERT: r 29 GLU cc_start: 0.8873 (pm20) cc_final: 0.8407 (pm20) REVERT: r 59 LEU cc_start: 0.8883 (mt) cc_final: 0.8548 (mt) REVERT: s 7 ASN cc_start: 0.6572 (m-40) cc_final: 0.5468 (p0) REVERT: s 23 THR cc_start: 0.8619 (m) cc_final: 0.8288 (m) REVERT: s 27 GLN cc_start: 0.8471 (mt0) cc_final: 0.7726 (tm-30) REVERT: s 65 SER cc_start: 0.9009 (t) cc_final: 0.8688 (m) REVERT: s 69 LYS cc_start: 0.8543 (tptm) cc_final: 0.7376 (ttmt) REVERT: t 24 GLN cc_start: 0.8619 (tp40) cc_final: 0.8394 (tp40) REVERT: t 51 GLN cc_start: 0.8587 (tt0) cc_final: 0.6723 (mm110) REVERT: t 69 LYS cc_start: 0.9258 (tptm) cc_final: 0.8593 (mttt) REVERT: t 72 LYS cc_start: 0.9485 (tmtt) cc_final: 0.9192 (tttp) REVERT: u 30 LEU cc_start: 0.8894 (tp) cc_final: 0.8545 (tt) REVERT: u 49 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7350 (mm-30) REVERT: u 65 SER cc_start: 0.9170 (t) cc_final: 0.8951 (t) REVERT: u 69 LYS cc_start: 0.8989 (tptm) cc_final: 0.7558 (ttmt) REVERT: u 82 PHE cc_start: 0.8932 (m-80) cc_final: 0.8596 (m-80) REVERT: v 25 THR cc_start: 0.8447 (p) cc_final: 0.8088 (p) REVERT: v 27 GLN cc_start: 0.7953 (mt0) cc_final: 0.7649 (tp40) REVERT: v 32 LEU cc_start: 0.9301 (tp) cc_final: 0.9014 (tp) REVERT: v 36 LYS cc_start: 0.9038 (mttt) cc_final: 0.8745 (mttm) REVERT: v 53 LYS cc_start: 0.8896 (mmmt) cc_final: 0.8656 (mmmm) REVERT: v 69 LYS cc_start: 0.9096 (tptm) cc_final: 0.8096 (mttt) REVERT: w 47 LEU cc_start: 0.9139 (mm) cc_final: 0.8817 (mm) REVERT: w 57 TYR cc_start: 0.8906 (t80) cc_final: 0.8453 (t80) REVERT: w 61 ARG cc_start: 0.8370 (mmt180) cc_final: 0.6625 (ttp-170) REVERT: w 69 LYS cc_start: 0.9016 (tppt) cc_final: 0.7597 (tppt) REVERT: a0 103 LYS cc_start: 0.8117 (tttm) cc_final: 0.6997 (tptt) REVERT: d0 103 LYS cc_start: 0.9256 (ttmt) cc_final: 0.7909 (tptt) REVERT: e0 103 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8041 (tttt) REVERT: f0 103 LYS cc_start: 0.9231 (ttmt) cc_final: 0.8329 (tptt) REVERT: g0 103 LYS cc_start: 0.9060 (mtmt) cc_final: 0.7712 (tptt) REVERT: i0 103 LYS cc_start: 0.8957 (tttt) cc_final: 0.8683 (tptt) REVERT: k0 103 LYS cc_start: 0.8833 (ttmm) cc_final: 0.7695 (tptt) REVERT: k0 105 ARG cc_start: 0.8814 (ttm110) cc_final: 0.7321 (tmt170) REVERT: l0 103 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8207 (tptt) REVERT: m0 103 LYS cc_start: 0.9065 (mtpt) cc_final: 0.8181 (tptt) REVERT: n0 97 SER cc_start: 0.9052 (m) cc_final: 0.8792 (t) REVERT: p0 103 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8049 (tptt) REVERT: q0 103 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8308 (tptt) REVERT: r0 102 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8081 (mt-10) REVERT: r0 103 LYS cc_start: 0.8849 (ttmt) cc_final: 0.7584 (tptt) REVERT: t0 103 LYS cc_start: 0.8834 (ttmt) cc_final: 0.8139 (tptt) REVERT: t0 105 ARG cc_start: 0.9196 (ttm110) cc_final: 0.8043 (tpm170) REVERT: u0 100 ARG cc_start: 0.7900 (ttm110) cc_final: 0.7496 (tpt170) REVERT: u0 103 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8052 (tptt) REVERT: v0 92 THR cc_start: 0.8553 (m) cc_final: 0.8276 (m) REVERT: v0 103 LYS cc_start: 0.9247 (mttt) cc_final: 0.7800 (tptt) REVERT: w0 103 LYS cc_start: 0.8866 (ttmt) cc_final: 0.8355 (tptt) REVERT: x0 103 LYS cc_start: 0.8454 (ttmt) cc_final: 0.7908 (tptt) outliers start: 6 outliers final: 1 residues processed: 2218 average time/residue: 0.5093 time to fit residues: 1895.0914 Evaluate side-chains 1930 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1929 time to evaluate : 5.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 487 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 288 optimal weight: 0.9980 chunk 369 optimal weight: 1.9990 chunk 286 optimal weight: 0.5980 chunk 425 optimal weight: 1.9990 chunk 282 optimal weight: 4.9990 chunk 504 optimal weight: 0.4980 chunk 315 optimal weight: 0.8980 chunk 307 optimal weight: 6.9990 chunk 232 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN D 131 ASN E 106 HIS ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 247 HIS F 252 ASN ** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS O 44 GLN P 59 ASN R 19 GLN T 80 GLN U 80 GLN W 81 ASN Y 144 ASN ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 137 HIS 4 127 GLN 4 137 HIS ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 43 ASN ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN ** f 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 40 ASN ** m 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 81 ASN r 27 GLN r 64 GLN u 40 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44858 Z= 0.201 Angle : 0.626 14.543 60890 Z= 0.308 Chirality : 0.040 0.270 7369 Planarity : 0.004 0.072 7620 Dihedral : 4.201 88.546 5953 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.10 % Allowed : 1.16 % Favored : 98.74 % 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: 3.04 (0.12), residues: 5404 helix: 3.11 (0.08), residues: 4152 sheet: 1.21 (0.33), residues: 224 loop : -2.88 (0.17), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP r 10 HIS 0.006 0.001 HIS F 11 PHE 0.029 0.002 PHE v 19 TYR 0.034 0.001 TYR E 158 ARG 0.012 0.000 ARG V 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2197 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2192 time to evaluate : 5.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8507 (p) cc_final: 0.7706 (p) REVERT: A 36 MET cc_start: 0.8808 (ttp) cc_final: 0.8350 (tpp) REVERT: A 50 MET cc_start: 0.8158 (ttp) cc_final: 0.7871 (ttm) REVERT: A 68 ILE cc_start: 0.9540 (mt) cc_final: 0.9239 (mt) REVERT: A 69 GLU cc_start: 0.7825 (tp30) cc_final: 0.7245 (mm-30) REVERT: A 101 GLN cc_start: 0.8955 (tt0) cc_final: 0.8425 (tm-30) REVERT: A 142 TYR cc_start: 0.9110 (t80) cc_final: 0.8531 (t80) REVERT: A 146 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8964 (mm-30) REVERT: A 152 LYS cc_start: 0.9140 (tttt) cc_final: 0.8692 (mtmt) REVERT: A 205 LYS cc_start: 0.9086 (mttt) cc_final: 0.8065 (tttt) REVERT: B 65 LYS cc_start: 0.8573 (tttp) cc_final: 0.8131 (tmtt) REVERT: B 116 GLN cc_start: 0.8832 (tp40) cc_final: 0.8554 (tp40) REVERT: B 146 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 177 MET cc_start: 0.8067 (mtt) cc_final: 0.7752 (mtt) REVERT: C 25 THR cc_start: 0.9255 (p) cc_final: 0.8732 (t) REVERT: C 117 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7840 (tpt170) REVERT: C 146 GLU cc_start: 0.8569 (tp30) cc_final: 0.8303 (mm-30) REVERT: C 152 LYS cc_start: 0.8563 (tttt) cc_final: 0.8277 (tmtt) REVERT: D 2 LEU cc_start: 0.9194 (mt) cc_final: 0.8968 (mt) REVERT: D 6 SER cc_start: 0.8773 (m) cc_final: 0.8033 (p) REVERT: D 156 TYR cc_start: 0.8572 (m-10) cc_final: 0.8151 (m-10) REVERT: D 205 LYS cc_start: 0.8998 (mttt) cc_final: 0.8626 (mtmt) REVERT: E 44 GLN cc_start: 0.8302 (mp10) cc_final: 0.8036 (mp10) REVERT: E 64 MET cc_start: 0.8611 (mmm) cc_final: 0.8006 (mmm) REVERT: F 104 ASP cc_start: 0.8432 (t0) cc_final: 0.8186 (t0) REVERT: F 133 PHE cc_start: 0.9006 (t80) cc_final: 0.8505 (t80) REVERT: F 152 GLN cc_start: 0.9025 (tt0) cc_final: 0.8489 (tp-100) REVERT: F 153 LEU cc_start: 0.9494 (tp) cc_final: 0.9277 (tp) REVERT: F 170 ASN cc_start: 0.8403 (m110) cc_final: 0.8191 (m-40) REVERT: G 52 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8590 (mtmt) REVERT: G 79 MET cc_start: 0.8725 (mmm) cc_final: 0.8171 (mmm) REVERT: H 14 LEU cc_start: 0.8717 (tp) cc_final: 0.8457 (tp) REVERT: H 18 PHE cc_start: 0.7923 (m-80) cc_final: 0.7533 (m-80) REVERT: H 77 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7739 (tm-30) REVERT: H 79 MET cc_start: 0.8115 (mmp) cc_final: 0.7446 (mmp) REVERT: I 60 LEU cc_start: 0.8532 (mt) cc_final: 0.8300 (mt) REVERT: I 69 GLU cc_start: 0.7607 (tp30) cc_final: 0.6472 (tp30) REVERT: J 70 VAL cc_start: 0.9665 (t) cc_final: 0.9412 (p) REVERT: K 51 MET cc_start: 0.7776 (mmt) cc_final: 0.7553 (mmt) REVERT: K 132 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8174 (mttt) REVERT: N 33 LYS cc_start: 0.8621 (mmmm) cc_final: 0.7992 (mmtt) REVERT: N 58 LEU cc_start: 0.9199 (mt) cc_final: 0.8883 (mt) REVERT: N 68 THR cc_start: 0.8884 (m) cc_final: 0.8580 (t) REVERT: O 41 THR cc_start: 0.8682 (t) cc_final: 0.8380 (m) REVERT: P 46 SER cc_start: 0.9489 (m) cc_final: 0.9226 (t) REVERT: P 56 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7133 (tm-30) REVERT: P 57 SER cc_start: 0.9072 (m) cc_final: 0.8476 (p) REVERT: S 25 THR cc_start: 0.7639 (t) cc_final: 0.7429 (t) REVERT: S 37 LEU cc_start: 0.9062 (tp) cc_final: 0.8717 (tp) REVERT: T 30 LEU cc_start: 0.9169 (tp) cc_final: 0.8886 (tp) REVERT: T 50 TYR cc_start: 0.9047 (t80) cc_final: 0.8802 (t80) REVERT: V 32 LEU cc_start: 0.8661 (mt) cc_final: 0.8311 (tt) REVERT: V 50 TYR cc_start: 0.9190 (t80) cc_final: 0.8952 (t80) REVERT: V 64 GLN cc_start: 0.8569 (tt0) cc_final: 0.8283 (tt0) REVERT: W 39 LYS cc_start: 0.8244 (mttt) cc_final: 0.7611 (mptt) REVERT: W 43 ASN cc_start: 0.8534 (t0) cc_final: 0.7835 (t0) REVERT: Y 112 SER cc_start: 0.7954 (p) cc_final: 0.7613 (m) REVERT: Y 123 ASN cc_start: 0.8673 (t0) cc_final: 0.8411 (t0) REVERT: Y 127 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7547 (tm-30) REVERT: Y 131 ASP cc_start: 0.7823 (m-30) cc_final: 0.7377 (m-30) REVERT: Y 138 ARG cc_start: 0.8756 (mtp85) cc_final: 0.8523 (mtp85) REVERT: Z 133 ASN cc_start: 0.9174 (t0) cc_final: 0.8935 (t0) REVERT: 0 161 LEU cc_start: 0.9079 (tp) cc_final: 0.8595 (tp) REVERT: 2 127 GLN cc_start: 0.8244 (tp40) cc_final: 0.7949 (tp40) REVERT: 4 127 GLN cc_start: 0.7822 (tp40) cc_final: 0.7349 (tp-100) REVERT: 4 131 ASP cc_start: 0.8001 (p0) cc_final: 0.7362 (p0) REVERT: 4 142 ARG cc_start: 0.7771 (mmt-90) cc_final: 0.6648 (mmt90) REVERT: 4 150 PHE cc_start: 0.9120 (p90) cc_final: 0.8625 (p90) REVERT: 4 167 THR cc_start: 0.8673 (m) cc_final: 0.8460 (t) REVERT: 6 127 GLN cc_start: 0.8949 (tp40) cc_final: 0.8330 (tp40) REVERT: 6 138 ARG cc_start: 0.8410 (mtp85) cc_final: 0.7314 (mtm110) REVERT: 6 149 THR cc_start: 0.8981 (m) cc_final: 0.8160 (p) REVERT: 6 168 LEU cc_start: 0.8790 (tp) cc_final: 0.8434 (tp) REVERT: 8 111 ILE cc_start: 0.9293 (mt) cc_final: 0.9073 (mt) REVERT: 8 115 ILE cc_start: 0.8886 (mt) cc_final: 0.8662 (mm) REVERT: 8 144 ASN cc_start: 0.7870 (t0) cc_final: 0.7480 (t0) REVERT: x 149 THR cc_start: 0.9434 (t) cc_final: 0.9175 (p) REVERT: x 150 PHE cc_start: 0.9323 (p90) cc_final: 0.8716 (p90) REVERT: x 153 SER cc_start: 0.9565 (t) cc_final: 0.9024 (p) REVERT: x 168 LEU cc_start: 0.9369 (tp) cc_final: 0.9122 (tt) REVERT: y 115 ILE cc_start: 0.9338 (mt) cc_final: 0.9135 (mt) REVERT: y 158 LEU cc_start: 0.8257 (tp) cc_final: 0.7863 (mm) REVERT: y 160 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7810 (mm-30) REVERT: y 164 ASN cc_start: 0.8662 (m-40) cc_final: 0.8385 (m-40) REVERT: z 112 SER cc_start: 0.9190 (p) cc_final: 0.8768 (m) REVERT: z 127 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7941 (tm-30) REVERT: z 138 ARG cc_start: 0.8252 (ttp-110) cc_final: 0.7959 (ttp-110) REVERT: z 149 THR cc_start: 0.9010 (m) cc_final: 0.8641 (t) REVERT: z 151 TYR cc_start: 0.8727 (t80) cc_final: 0.8249 (t80) REVERT: 1 130 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8205 (mmtt) REVERT: 1 133 ASN cc_start: 0.8660 (m-40) cc_final: 0.8315 (t0) REVERT: 3 115 ILE cc_start: 0.8828 (mt) cc_final: 0.8172 (mt) REVERT: 3 118 GLU cc_start: 0.6030 (tp30) cc_final: 0.5743 (tp30) REVERT: 7 168 LEU cc_start: 0.9126 (tp) cc_final: 0.8916 (tp) REVERT: 9 128 TYR cc_start: 0.8798 (t80) cc_final: 0.8504 (t80) REVERT: a 26 LEU cc_start: 0.8900 (tp) cc_final: 0.8643 (tp) REVERT: a 72 LYS cc_start: 0.9589 (tmtt) cc_final: 0.9108 (tptp) REVERT: a 80 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8316 (tm-30) REVERT: b 3 VAL cc_start: 0.5922 (p) cc_final: 0.5697 (p) REVERT: b 45 GLN cc_start: 0.8515 (tp40) cc_final: 0.7691 (tm-30) REVERT: b 49 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6906 (mm-30) REVERT: b 59 LEU cc_start: 0.9312 (mp) cc_final: 0.9102 (mp) REVERT: b 65 SER cc_start: 0.9244 (m) cc_final: 0.8873 (t) REVERT: c 59 LEU cc_start: 0.9470 (mt) cc_final: 0.9000 (mt) REVERT: c 80 GLN cc_start: 0.8765 (tp40) cc_final: 0.8290 (tp40) REVERT: d 43 ASN cc_start: 0.8402 (t0) cc_final: 0.8175 (t0) REVERT: d 57 TYR cc_start: 0.8999 (t80) cc_final: 0.8500 (t80) REVERT: d 71 ILE cc_start: 0.8690 (mm) cc_final: 0.8162 (mm) REVERT: d 72 LYS cc_start: 0.9156 (tttm) cc_final: 0.8948 (tttt) REVERT: d 75 ASP cc_start: 0.8283 (m-30) cc_final: 0.7949 (m-30) REVERT: e 42 SER cc_start: 0.9474 (m) cc_final: 0.9048 (t) REVERT: e 56 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8251 (tt0) REVERT: e 79 ILE cc_start: 0.9385 (tp) cc_final: 0.9177 (tt) REVERT: f 37 LEU cc_start: 0.8653 (tt) cc_final: 0.8295 (tt) REVERT: f 75 ASP cc_start: 0.7702 (m-30) cc_final: 0.7495 (m-30) REVERT: f 80 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8076 (tm-30) REVERT: g 25 THR cc_start: 0.8113 (p) cc_final: 0.7912 (p) REVERT: g 79 ILE cc_start: 0.9195 (mm) cc_final: 0.8946 (mm) REVERT: h 11 THR cc_start: 0.8695 (m) cc_final: 0.7852 (m) REVERT: i 80 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7997 (tm-30) REVERT: j 14 SER cc_start: 0.9115 (m) cc_final: 0.8662 (p) REVERT: j 80 GLN cc_start: 0.9179 (tp-100) cc_final: 0.8922 (tp-100) REVERT: k 37 LEU cc_start: 0.8939 (tp) cc_final: 0.8634 (tt) REVERT: k 50 TYR cc_start: 0.9288 (t80) cc_final: 0.8911 (t80) REVERT: k 80 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8089 (tp40) REVERT: l 16 SER cc_start: 0.8881 (m) cc_final: 0.8079 (t) REVERT: l 20 ASP cc_start: 0.7542 (m-30) cc_final: 0.7228 (m-30) REVERT: l 25 THR cc_start: 0.8658 (p) cc_final: 0.7872 (p) REVERT: l 45 GLN cc_start: 0.8074 (tp40) cc_final: 0.7548 (tp40) REVERT: l 50 TYR cc_start: 0.9169 (t80) cc_final: 0.8766 (t80) REVERT: l 59 LEU cc_start: 0.9454 (mt) cc_final: 0.9112 (mp) REVERT: m 20 ASP cc_start: 0.7798 (m-30) cc_final: 0.7336 (m-30) REVERT: m 50 TYR cc_start: 0.8725 (t80) cc_final: 0.8476 (t80) REVERT: m 75 ASP cc_start: 0.8338 (m-30) cc_final: 0.7809 (m-30) REVERT: n 3 VAL cc_start: 0.8550 (t) cc_final: 0.8209 (m) REVERT: n 29 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7108 (tm-30) REVERT: n 53 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8331 (mmtm) REVERT: n 71 ILE cc_start: 0.9431 (mm) cc_final: 0.9197 (mm) REVERT: n 75 ASP cc_start: 0.8475 (m-30) cc_final: 0.8123 (m-30) REVERT: n 80 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8018 (tm-30) REVERT: o 50 TYR cc_start: 0.9329 (t80) cc_final: 0.8693 (t80) REVERT: p 25 THR cc_start: 0.8352 (p) cc_final: 0.7623 (t) REVERT: p 75 ASP cc_start: 0.8622 (m-30) cc_final: 0.7952 (m-30) REVERT: q 32 LEU cc_start: 0.8144 (tp) cc_final: 0.7785 (tp) REVERT: q 36 LYS cc_start: 0.8681 (mttt) cc_final: 0.8387 (mtmt) REVERT: q 50 TYR cc_start: 0.8391 (t80) cc_final: 0.8184 (t80) REVERT: r 29 GLU cc_start: 0.8934 (pm20) cc_final: 0.8667 (pm20) REVERT: r 72 LYS cc_start: 0.9296 (tmtt) cc_final: 0.8923 (tptp) REVERT: s 7 ASN cc_start: 0.6709 (m-40) cc_final: 0.5648 (p0) REVERT: s 23 THR cc_start: 0.8630 (m) cc_final: 0.8251 (m) REVERT: s 27 GLN cc_start: 0.8499 (mt0) cc_final: 0.7732 (tm-30) REVERT: s 65 SER cc_start: 0.9048 (t) cc_final: 0.8707 (m) REVERT: s 69 LYS cc_start: 0.7895 (tptm) cc_final: 0.7367 (ttmt) REVERT: t 23 THR cc_start: 0.9076 (t) cc_final: 0.8816 (t) REVERT: t 24 GLN cc_start: 0.8672 (tp40) cc_final: 0.8430 (tp40) REVERT: t 51 GLN cc_start: 0.8607 (tt0) cc_final: 0.6705 (mm110) REVERT: t 60 TYR cc_start: 0.8341 (t80) cc_final: 0.8049 (t80) REVERT: t 69 LYS cc_start: 0.9241 (tptm) cc_final: 0.8581 (mttt) REVERT: t 72 LYS cc_start: 0.9481 (tmtt) cc_final: 0.9227 (tttp) REVERT: u 30 LEU cc_start: 0.8787 (tp) cc_final: 0.8482 (tt) REVERT: u 49 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7195 (mm-30) REVERT: u 65 SER cc_start: 0.9105 (t) cc_final: 0.8888 (t) REVERT: u 69 LYS cc_start: 0.8911 (tptm) cc_final: 0.7513 (ttmt) REVERT: u 82 PHE cc_start: 0.8960 (m-80) cc_final: 0.8530 (m-80) REVERT: v 25 THR cc_start: 0.8407 (p) cc_final: 0.7979 (p) REVERT: v 27 GLN cc_start: 0.7991 (mt0) cc_final: 0.7643 (tp40) REVERT: v 32 LEU cc_start: 0.9302 (tp) cc_final: 0.9020 (tp) REVERT: v 36 LYS cc_start: 0.9008 (mttt) cc_final: 0.8701 (mttm) REVERT: v 53 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8634 (mmmm) REVERT: v 69 LYS cc_start: 0.9115 (tptm) cc_final: 0.8167 (mttt) REVERT: w 57 TYR cc_start: 0.8921 (t80) cc_final: 0.8484 (t80) REVERT: w 61 ARG cc_start: 0.8345 (mmt180) cc_final: 0.6666 (ttp-170) REVERT: w 69 LYS cc_start: 0.9029 (tppt) cc_final: 0.7421 (tppt) REVERT: a0 103 LYS cc_start: 0.8136 (tttm) cc_final: 0.7041 (tptt) REVERT: d0 103 LYS cc_start: 0.9259 (ttmt) cc_final: 0.7901 (tptt) REVERT: e0 103 LYS cc_start: 0.8691 (ttmt) cc_final: 0.7876 (tttt) REVERT: f0 103 LYS cc_start: 0.9218 (ttmt) cc_final: 0.8308 (tptt) REVERT: g0 103 LYS cc_start: 0.9081 (mtmt) cc_final: 0.7752 (tptt) REVERT: i0 103 LYS cc_start: 0.8960 (tttt) cc_final: 0.8671 (tptt) REVERT: k0 103 LYS cc_start: 0.8876 (ttmm) cc_final: 0.7654 (tptt) REVERT: l0 103 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8210 (tptt) REVERT: m0 103 LYS cc_start: 0.9056 (mtpt) cc_final: 0.8180 (tptt) REVERT: n0 97 SER cc_start: 0.9031 (m) cc_final: 0.8810 (t) REVERT: n0 103 LYS cc_start: 0.8775 (ttpt) cc_final: 0.8303 (ttpt) REVERT: p0 103 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8068 (tptt) REVERT: q0 103 LYS cc_start: 0.9010 (ttmt) cc_final: 0.8319 (tptt) REVERT: r0 102 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8079 (mt-10) REVERT: r0 103 LYS cc_start: 0.8852 (ttmt) cc_final: 0.7572 (tptt) REVERT: t0 103 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8084 (tptt) REVERT: t0 105 ARG cc_start: 0.9199 (ttm110) cc_final: 0.8044 (tpm170) REVERT: u0 103 LYS cc_start: 0.9110 (ttmt) cc_final: 0.8025 (tptt) REVERT: v0 92 THR cc_start: 0.8579 (m) cc_final: 0.8281 (m) REVERT: v0 103 LYS cc_start: 0.9273 (mttt) cc_final: 0.7831 (tptt) REVERT: w0 103 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8322 (tptt) REVERT: x0 103 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7928 (tptt) outliers start: 5 outliers final: 0 residues processed: 2192 average time/residue: 0.5066 time to fit residues: 1867.4485 Evaluate side-chains 1893 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1893 time to evaluate : 5.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 311 optimal weight: 3.9990 chunk 201 optimal weight: 0.6980 chunk 301 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 320 optimal weight: 0.8980 chunk 343 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 396 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN B 213 ASN D 116 GLN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 247 HIS F 252 ASN J 76 HIS O 44 GLN P 59 ASN R 19 GLN ** S 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 81 ASN Y 144 ASN ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 137 HIS 4 137 HIS ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 119 ASN ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 24 GLN b 43 ASN b 64 GLN ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 51 GLN g 64 GLN g 81 ASN i 24 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 27 GLN m 81 ASN r 24 GLN r 64 GLN u 40 ASN v 81 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 44858 Z= 0.229 Angle : 0.641 12.302 60890 Z= 0.318 Chirality : 0.041 0.194 7369 Planarity : 0.004 0.075 7620 Dihedral : 4.250 86.790 5953 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.10 % Allowed : 0.86 % Favored : 99.04 % 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: 2.98 (0.12), residues: 5404 helix: 3.05 (0.08), residues: 4154 sheet: 1.17 (0.33), residues: 224 loop : -2.85 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP w 10 HIS 0.006 0.001 HIS F 11 PHE 0.030 0.002 PHE r 19 TYR 0.025 0.001 TYR O 3 ARG 0.016 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2162 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2157 time to evaluate : 5.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8518 (p) cc_final: 0.7717 (p) REVERT: A 50 MET cc_start: 0.8205 (ttp) cc_final: 0.7892 (ttm) REVERT: A 68 ILE cc_start: 0.9554 (mt) cc_final: 0.9252 (mt) REVERT: A 69 GLU cc_start: 0.7829 (tp30) cc_final: 0.7308 (mm-30) REVERT: A 101 GLN cc_start: 0.8980 (tt0) cc_final: 0.8679 (tm-30) REVERT: A 142 TYR cc_start: 0.9118 (t80) cc_final: 0.8601 (t80) REVERT: A 152 LYS cc_start: 0.9170 (tttt) cc_final: 0.8722 (ttmt) REVERT: A 205 LYS cc_start: 0.9132 (mttt) cc_final: 0.8162 (tttt) REVERT: B 65 LYS cc_start: 0.8604 (tttp) cc_final: 0.8144 (tmtt) REVERT: B 116 GLN cc_start: 0.8868 (tp40) cc_final: 0.8596 (tp40) REVERT: B 177 MET cc_start: 0.8174 (mtt) cc_final: 0.7890 (mtt) REVERT: B 190 LYS cc_start: 0.9231 (mtmt) cc_final: 0.8066 (mtmm) REVERT: C 25 THR cc_start: 0.9178 (p) cc_final: 0.8732 (t) REVERT: C 117 ARG cc_start: 0.8334 (mtt180) cc_final: 0.7850 (tpt170) REVERT: C 146 GLU cc_start: 0.8553 (tp30) cc_final: 0.8283 (mm-30) REVERT: C 152 LYS cc_start: 0.8703 (tttt) cc_final: 0.8446 (tmtt) REVERT: D 2 LEU cc_start: 0.9211 (mt) cc_final: 0.8971 (mt) REVERT: D 6 SER cc_start: 0.8801 (m) cc_final: 0.8089 (p) REVERT: D 17 LEU cc_start: 0.9329 (tp) cc_final: 0.8889 (tt) REVERT: D 156 TYR cc_start: 0.8693 (m-10) cc_final: 0.8318 (m-10) REVERT: D 205 LYS cc_start: 0.8984 (mttt) cc_final: 0.8549 (mttt) REVERT: E 44 GLN cc_start: 0.8306 (mp10) cc_final: 0.8081 (mp10) REVERT: E 64 MET cc_start: 0.8714 (mmm) cc_final: 0.8069 (mmm) REVERT: F 133 PHE cc_start: 0.9050 (t80) cc_final: 0.8456 (t80) REVERT: F 152 GLN cc_start: 0.9041 (tt0) cc_final: 0.8518 (tp-100) REVERT: F 153 LEU cc_start: 0.9514 (tp) cc_final: 0.9304 (tp) REVERT: G 52 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8621 (mtmt) REVERT: G 79 MET cc_start: 0.8674 (mmm) cc_final: 0.7987 (mmm) REVERT: H 14 LEU cc_start: 0.8664 (tp) cc_final: 0.8461 (tp) REVERT: H 18 PHE cc_start: 0.8095 (m-80) cc_final: 0.7761 (m-80) REVERT: H 77 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7674 (tm-30) REVERT: H 79 MET cc_start: 0.8103 (mmp) cc_final: 0.7502 (mmp) REVERT: I 60 LEU cc_start: 0.8543 (mt) cc_final: 0.8312 (mt) REVERT: I 69 GLU cc_start: 0.7660 (tp30) cc_final: 0.6494 (tp30) REVERT: K 132 LYS cc_start: 0.8593 (mmtp) cc_final: 0.8172 (mttt) REVERT: N 58 LEU cc_start: 0.9215 (mt) cc_final: 0.8861 (mt) REVERT: N 68 THR cc_start: 0.8934 (m) cc_final: 0.8606 (t) REVERT: O 41 THR cc_start: 0.8681 (t) cc_final: 0.8359 (m) REVERT: P 44 GLN cc_start: 0.8166 (tt0) cc_final: 0.7853 (tt0) REVERT: P 56 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7690 (tm-30) REVERT: P 57 SER cc_start: 0.9062 (m) cc_final: 0.8461 (p) REVERT: R 50 GLU cc_start: 0.8220 (tp30) cc_final: 0.7917 (tm-30) REVERT: S 25 THR cc_start: 0.7690 (t) cc_final: 0.7462 (t) REVERT: S 37 LEU cc_start: 0.9081 (tp) cc_final: 0.8738 (tp) REVERT: T 30 LEU cc_start: 0.9168 (tp) cc_final: 0.8856 (tp) REVERT: T 50 TYR cc_start: 0.9022 (t80) cc_final: 0.8817 (t80) REVERT: V 32 LEU cc_start: 0.8692 (mt) cc_final: 0.8311 (tt) REVERT: W 39 LYS cc_start: 0.8207 (mttt) cc_final: 0.7580 (mptt) REVERT: W 43 ASN cc_start: 0.8502 (t0) cc_final: 0.7855 (t0) REVERT: Y 112 SER cc_start: 0.7989 (p) cc_final: 0.7641 (m) REVERT: Y 123 ASN cc_start: 0.8683 (t0) cc_final: 0.8412 (t0) REVERT: Y 127 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7562 (tm-30) REVERT: Y 131 ASP cc_start: 0.7918 (m-30) cc_final: 0.7471 (m-30) REVERT: Z 133 ASN cc_start: 0.9182 (t0) cc_final: 0.8938 (t0) REVERT: 0 161 LEU cc_start: 0.9070 (tp) cc_final: 0.8638 (tp) REVERT: 2 127 GLN cc_start: 0.8362 (tp40) cc_final: 0.7999 (tp40) REVERT: 4 127 GLN cc_start: 0.7811 (tp40) cc_final: 0.7352 (tp-100) REVERT: 4 131 ASP cc_start: 0.8003 (p0) cc_final: 0.7393 (p0) REVERT: 4 142 ARG cc_start: 0.7990 (mmt-90) cc_final: 0.6748 (mmt90) REVERT: 4 150 PHE cc_start: 0.9107 (p90) cc_final: 0.8592 (p90) REVERT: 6 127 GLN cc_start: 0.8885 (tp40) cc_final: 0.8274 (tp40) REVERT: 6 138 ARG cc_start: 0.8405 (mtp85) cc_final: 0.7519 (mtm110) REVERT: 6 149 THR cc_start: 0.8954 (m) cc_final: 0.8127 (p) REVERT: 6 168 LEU cc_start: 0.8779 (tp) cc_final: 0.8448 (tp) REVERT: 8 144 ASN cc_start: 0.7876 (t0) cc_final: 0.7441 (t0) REVERT: x 149 THR cc_start: 0.9438 (t) cc_final: 0.9171 (p) REVERT: x 150 PHE cc_start: 0.9323 (p90) cc_final: 0.8665 (p90) REVERT: x 153 SER cc_start: 0.9565 (t) cc_final: 0.9033 (p) REVERT: x 168 LEU cc_start: 0.9413 (tp) cc_final: 0.9187 (tt) REVERT: y 115 ILE cc_start: 0.9382 (mt) cc_final: 0.9119 (mt) REVERT: y 158 LEU cc_start: 0.8269 (tp) cc_final: 0.7887 (mm) REVERT: y 160 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7801 (mm-30) REVERT: y 164 ASN cc_start: 0.8674 (m-40) cc_final: 0.8237 (m-40) REVERT: z 127 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8026 (tm-30) REVERT: z 149 THR cc_start: 0.8985 (m) cc_final: 0.8663 (t) REVERT: 1 130 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8233 (mmtt) REVERT: 1 133 ASN cc_start: 0.8651 (m-40) cc_final: 0.8303 (t0) REVERT: 3 115 ILE cc_start: 0.8578 (mt) cc_final: 0.8301 (mt) REVERT: 5 131 ASP cc_start: 0.8194 (p0) cc_final: 0.7861 (p0) REVERT: 7 168 LEU cc_start: 0.9113 (tp) cc_final: 0.8874 (tp) REVERT: 9 128 TYR cc_start: 0.8797 (t80) cc_final: 0.8563 (t80) REVERT: a 26 LEU cc_start: 0.8904 (tp) cc_final: 0.8627 (tp) REVERT: a 31 THR cc_start: 0.7947 (m) cc_final: 0.7487 (m) REVERT: a 72 LYS cc_start: 0.9582 (tmtt) cc_final: 0.9092 (tptp) REVERT: a 80 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8289 (tm-30) REVERT: b 45 GLN cc_start: 0.8540 (tp40) cc_final: 0.7709 (tm-30) REVERT: b 49 GLU cc_start: 0.7645 (mm-30) cc_final: 0.6912 (mm-30) REVERT: b 64 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: b 65 SER cc_start: 0.9240 (m) cc_final: 0.8873 (t) REVERT: c 59 LEU cc_start: 0.9480 (mt) cc_final: 0.9022 (mt) REVERT: c 80 GLN cc_start: 0.8749 (tp40) cc_final: 0.8325 (tp40) REVERT: d 43 ASN cc_start: 0.8389 (t0) cc_final: 0.7969 (t0) REVERT: d 57 TYR cc_start: 0.9042 (t80) cc_final: 0.8543 (t80) REVERT: d 75 ASP cc_start: 0.8269 (m-30) cc_final: 0.7982 (m-30) REVERT: e 42 SER cc_start: 0.9478 (m) cc_final: 0.9014 (t) REVERT: e 79 ILE cc_start: 0.9421 (tp) cc_final: 0.9114 (tt) REVERT: f 17 GLU cc_start: 0.7470 (tm-30) cc_final: 0.6953 (tm-30) REVERT: f 37 LEU cc_start: 0.8684 (tt) cc_final: 0.8345 (tt) REVERT: f 80 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8078 (tm-30) REVERT: g 49 GLU cc_start: 0.8376 (mp0) cc_final: 0.8145 (mp0) REVERT: g 79 ILE cc_start: 0.9210 (mm) cc_final: 0.8956 (mm) REVERT: h 11 THR cc_start: 0.7873 (m) cc_final: 0.7647 (m) REVERT: h 55 SER cc_start: 0.9353 (m) cc_final: 0.9062 (m) REVERT: h 59 LEU cc_start: 0.9422 (mp) cc_final: 0.8991 (mp) REVERT: i 80 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8047 (tm-30) REVERT: j 14 SER cc_start: 0.9064 (m) cc_final: 0.8625 (p) REVERT: j 80 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8952 (tp-100) REVERT: k 37 LEU cc_start: 0.8973 (tp) cc_final: 0.8666 (tt) REVERT: k 50 TYR cc_start: 0.9313 (t80) cc_final: 0.8927 (t80) REVERT: k 80 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8136 (tp40) REVERT: l 16 SER cc_start: 0.9002 (m) cc_final: 0.8219 (t) REVERT: l 20 ASP cc_start: 0.7554 (m-30) cc_final: 0.7316 (m-30) REVERT: l 25 THR cc_start: 0.8678 (p) cc_final: 0.7986 (p) REVERT: l 45 GLN cc_start: 0.8115 (tp40) cc_final: 0.7590 (tp40) REVERT: l 50 TYR cc_start: 0.9194 (t80) cc_final: 0.8800 (t80) REVERT: l 59 LEU cc_start: 0.9447 (mt) cc_final: 0.9193 (mp) REVERT: m 20 ASP cc_start: 0.7906 (m-30) cc_final: 0.7347 (m-30) REVERT: m 50 TYR cc_start: 0.8759 (t80) cc_final: 0.8496 (t80) REVERT: m 75 ASP cc_start: 0.8364 (m-30) cc_final: 0.7832 (m-30) REVERT: n 3 VAL cc_start: 0.8608 (t) cc_final: 0.8286 (m) REVERT: n 29 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7164 (tm-30) REVERT: n 49 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6965 (tm-30) REVERT: n 53 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8508 (mmtm) REVERT: n 71 ILE cc_start: 0.9414 (mm) cc_final: 0.9184 (mm) REVERT: n 75 ASP cc_start: 0.8514 (m-30) cc_final: 0.8136 (m-30) REVERT: n 80 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8011 (tm-30) REVERT: o 14 SER cc_start: 0.8753 (t) cc_final: 0.8374 (p) REVERT: o 50 TYR cc_start: 0.9346 (t80) cc_final: 0.8696 (t80) REVERT: p 25 THR cc_start: 0.8344 (p) cc_final: 0.7605 (t) REVERT: p 75 ASP cc_start: 0.8664 (m-30) cc_final: 0.8008 (m-30) REVERT: q 32 LEU cc_start: 0.8226 (tp) cc_final: 0.7848 (tp) REVERT: q 36 LYS cc_start: 0.8667 (mttt) cc_final: 0.8414 (mtmt) REVERT: q 50 TYR cc_start: 0.8402 (t80) cc_final: 0.8137 (t80) REVERT: s 7 ASN cc_start: 0.6797 (m-40) cc_final: 0.5723 (p0) REVERT: s 23 THR cc_start: 0.8730 (m) cc_final: 0.8351 (m) REVERT: s 27 GLN cc_start: 0.8479 (mt0) cc_final: 0.7602 (tm-30) REVERT: s 65 SER cc_start: 0.9138 (t) cc_final: 0.8763 (m) REVERT: s 69 LYS cc_start: 0.8641 (tptm) cc_final: 0.7423 (ttmt) REVERT: t 23 THR cc_start: 0.9082 (t) cc_final: 0.8758 (t) REVERT: t 24 GLN cc_start: 0.8716 (tp40) cc_final: 0.8470 (tp40) REVERT: t 51 GLN cc_start: 0.8675 (tt0) cc_final: 0.6930 (mm110) REVERT: t 60 TYR cc_start: 0.8429 (t80) cc_final: 0.8155 (t80) REVERT: t 69 LYS cc_start: 0.9263 (tptm) cc_final: 0.8593 (mttt) REVERT: t 72 LYS cc_start: 0.9491 (tmtt) cc_final: 0.9234 (tttp) REVERT: u 30 LEU cc_start: 0.8919 (tp) cc_final: 0.8659 (tt) REVERT: u 46 LEU cc_start: 0.8694 (tp) cc_final: 0.8461 (tp) REVERT: u 49 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7353 (tp30) REVERT: u 65 SER cc_start: 0.9190 (t) cc_final: 0.8953 (t) REVERT: u 69 LYS cc_start: 0.8918 (tptm) cc_final: 0.7523 (ttmt) REVERT: u 82 PHE cc_start: 0.9010 (m-80) cc_final: 0.8487 (m-80) REVERT: v 25 THR cc_start: 0.8453 (p) cc_final: 0.8038 (p) REVERT: v 32 LEU cc_start: 0.9317 (tp) cc_final: 0.9040 (tp) REVERT: v 36 LYS cc_start: 0.9019 (mttt) cc_final: 0.8720 (mttm) REVERT: v 53 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8681 (mmmm) REVERT: v 69 LYS cc_start: 0.9091 (tptm) cc_final: 0.8172 (mttt) REVERT: w 57 TYR cc_start: 0.8942 (t80) cc_final: 0.8487 (t80) REVERT: w 61 ARG cc_start: 0.8386 (mmt180) cc_final: 0.6694 (ttp-170) REVERT: w 69 LYS cc_start: 0.8905 (tppt) cc_final: 0.7390 (tppt) REVERT: a0 103 LYS cc_start: 0.8143 (tttm) cc_final: 0.7049 (tptt) REVERT: d0 103 LYS cc_start: 0.9251 (ttmt) cc_final: 0.7903 (tptt) REVERT: e0 103 LYS cc_start: 0.8323 (ttmt) cc_final: 0.7979 (tttt) REVERT: f0 103 LYS cc_start: 0.9232 (ttmt) cc_final: 0.8330 (tptt) REVERT: g0 103 LYS cc_start: 0.9078 (mtmt) cc_final: 0.7772 (tptt) REVERT: i0 103 LYS cc_start: 0.8985 (tttt) cc_final: 0.8692 (tptt) REVERT: k0 103 LYS cc_start: 0.8872 (ttmm) cc_final: 0.7946 (tptt) REVERT: l0 103 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8228 (tptt) REVERT: m0 103 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8185 (tptt) REVERT: n0 97 SER cc_start: 0.9012 (m) cc_final: 0.8799 (t) REVERT: n0 103 LYS cc_start: 0.8862 (ttpt) cc_final: 0.8330 (ttpt) REVERT: p0 103 LYS cc_start: 0.8880 (ttpt) cc_final: 0.8093 (tptt) REVERT: q0 103 LYS cc_start: 0.9050 (ttmt) cc_final: 0.8348 (tptt) REVERT: r0 102 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8099 (mt-10) REVERT: r0 103 LYS cc_start: 0.8878 (ttmt) cc_final: 0.7599 (tptt) REVERT: t0 103 LYS cc_start: 0.8886 (ttmt) cc_final: 0.8089 (tptt) REVERT: t0 105 ARG cc_start: 0.9217 (ttm110) cc_final: 0.8024 (tpm170) REVERT: u0 103 LYS cc_start: 0.9114 (ttmt) cc_final: 0.8020 (tptt) REVERT: v0 92 THR cc_start: 0.8579 (m) cc_final: 0.8288 (m) REVERT: v0 103 LYS cc_start: 0.9269 (mttt) cc_final: 0.7831 (tptt) REVERT: w0 103 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8306 (tptt) REVERT: x0 103 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7790 (tptt) outliers start: 5 outliers final: 1 residues processed: 2158 average time/residue: 0.5081 time to fit residues: 1848.1017 Evaluate side-chains 1880 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1878 time to evaluate : 4.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 458 optimal weight: 0.8980 chunk 482 optimal weight: 0.9980 chunk 440 optimal weight: 2.9990 chunk 469 optimal weight: 0.5980 chunk 282 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 368 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 424 optimal weight: 0.9990 chunk 444 optimal weight: 2.9990 chunk 468 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN B 213 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN D 131 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN J 76 HIS K 162 GLN O 44 GLN P 59 ASN R 19 GLN W 81 ASN Y 144 ASN ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 137 HIS 4 137 HIS ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 24 GLN ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 64 GLN ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 40 ASN f 51 GLN g 81 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 27 GLN m 81 ASN o 24 GLN u 40 ASN v 81 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 44858 Z= 0.205 Angle : 0.648 10.022 60890 Z= 0.319 Chirality : 0.040 0.377 7369 Planarity : 0.004 0.077 7620 Dihedral : 4.225 85.957 5953 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 0.06 % Allowed : 0.84 % Favored : 99.10 % 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: 2.96 (0.12), residues: 5404 helix: 3.03 (0.08), residues: 4153 sheet: 1.16 (0.33), residues: 224 loop : -2.81 (0.17), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP w 10 HIS 0.006 0.001 HIS F 11 PHE 0.031 0.002 PHE o 19 TYR 0.038 0.001 TYR E 158 ARG 0.010 0.000 ARG K 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2155 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2152 time to evaluate : 5.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8637 (p) cc_final: 0.7855 (p) REVERT: A 50 MET cc_start: 0.8149 (ttp) cc_final: 0.7867 (ttm) REVERT: A 68 ILE cc_start: 0.9582 (mt) cc_final: 0.9294 (mt) REVERT: A 69 GLU cc_start: 0.7975 (tp30) cc_final: 0.7219 (mm-30) REVERT: A 101 GLN cc_start: 0.8950 (tt0) cc_final: 0.8428 (tm-30) REVERT: A 142 TYR cc_start: 0.9136 (t80) cc_final: 0.8666 (t80) REVERT: A 152 LYS cc_start: 0.9117 (tttt) cc_final: 0.8736 (ttmt) REVERT: A 205 LYS cc_start: 0.9114 (mttt) cc_final: 0.8146 (tttt) REVERT: B 65 LYS cc_start: 0.8597 (tttp) cc_final: 0.8116 (tmtt) REVERT: B 116 GLN cc_start: 0.8890 (tp40) cc_final: 0.8685 (tp40) REVERT: B 190 LYS cc_start: 0.9238 (mtmt) cc_final: 0.8072 (mtmm) REVERT: C 25 THR cc_start: 0.9079 (p) cc_final: 0.8575 (t) REVERT: C 72 TYR cc_start: 0.5715 (t80) cc_final: 0.5314 (m-10) REVERT: C 117 ARG cc_start: 0.8338 (mtt180) cc_final: 0.7843 (tpt170) REVERT: C 146 GLU cc_start: 0.8591 (tp30) cc_final: 0.8298 (mm-30) REVERT: C 152 LYS cc_start: 0.8695 (tttt) cc_final: 0.8472 (tmtt) REVERT: D 6 SER cc_start: 0.8727 (m) cc_final: 0.8031 (p) REVERT: D 17 LEU cc_start: 0.9258 (tp) cc_final: 0.8877 (tt) REVERT: D 156 TYR cc_start: 0.8601 (m-10) cc_final: 0.8200 (m-10) REVERT: E 44 GLN cc_start: 0.8384 (mp10) cc_final: 0.8180 (mp10) REVERT: E 64 MET cc_start: 0.8711 (mmm) cc_final: 0.8086 (mmm) REVERT: F 128 LYS cc_start: 0.8793 (pttt) cc_final: 0.8430 (tmmt) REVERT: F 133 PHE cc_start: 0.9061 (t80) cc_final: 0.8445 (t80) REVERT: F 152 GLN cc_start: 0.9001 (tt0) cc_final: 0.8490 (tp-100) REVERT: F 153 LEU cc_start: 0.9519 (tp) cc_final: 0.9302 (tp) REVERT: F 229 PHE cc_start: 0.8498 (t80) cc_final: 0.7998 (t80) REVERT: G 52 LYS cc_start: 0.8871 (mtmt) cc_final: 0.8595 (mtmt) REVERT: G 79 MET cc_start: 0.8706 (mmm) cc_final: 0.8174 (mmm) REVERT: H 18 PHE cc_start: 0.8067 (m-80) cc_final: 0.7788 (m-80) REVERT: H 77 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7665 (tm-30) REVERT: H 79 MET cc_start: 0.8142 (mmp) cc_final: 0.7510 (mmp) REVERT: H 81 LEU cc_start: 0.8501 (mt) cc_final: 0.8300 (mt) REVERT: I 60 LEU cc_start: 0.8535 (mt) cc_final: 0.8304 (mt) REVERT: I 69 GLU cc_start: 0.7631 (tp30) cc_final: 0.6477 (tp30) REVERT: J 70 VAL cc_start: 0.9645 (t) cc_final: 0.9419 (p) REVERT: K 132 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8072 (mttt) REVERT: N 33 LYS cc_start: 0.8636 (mmmm) cc_final: 0.7984 (mmtt) REVERT: N 58 LEU cc_start: 0.9234 (mt) cc_final: 0.8920 (mt) REVERT: N 68 THR cc_start: 0.8836 (m) cc_final: 0.8595 (t) REVERT: O 41 THR cc_start: 0.8664 (t) cc_final: 0.8359 (m) REVERT: P 44 GLN cc_start: 0.8134 (tt0) cc_final: 0.7831 (tt0) REVERT: P 56 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7480 (tm-30) REVERT: P 57 SER cc_start: 0.9067 (m) cc_final: 0.8437 (p) REVERT: R 50 GLU cc_start: 0.8188 (tp30) cc_final: 0.7859 (tm-30) REVERT: S 25 THR cc_start: 0.7627 (t) cc_final: 0.7414 (t) REVERT: S 37 LEU cc_start: 0.9055 (tp) cc_final: 0.8727 (tp) REVERT: T 30 LEU cc_start: 0.9137 (tp) cc_final: 0.8838 (tp) REVERT: T 37 LEU cc_start: 0.8805 (tt) cc_final: 0.8589 (tp) REVERT: V 32 LEU cc_start: 0.8665 (mt) cc_final: 0.8292 (tt) REVERT: W 39 LYS cc_start: 0.8224 (mttt) cc_final: 0.7599 (mptt) REVERT: W 43 ASN cc_start: 0.8485 (t0) cc_final: 0.7829 (t0) REVERT: Y 112 SER cc_start: 0.8044 (p) cc_final: 0.7701 (m) REVERT: Y 123 ASN cc_start: 0.8652 (t0) cc_final: 0.8399 (t0) REVERT: Y 127 GLN cc_start: 0.7852 (tm-30) cc_final: 0.7525 (tm-30) REVERT: Y 131 ASP cc_start: 0.7851 (m-30) cc_final: 0.7397 (m-30) REVERT: Z 133 ASN cc_start: 0.9155 (t0) cc_final: 0.8912 (t0) REVERT: 0 133 ASN cc_start: 0.7942 (m-40) cc_final: 0.7624 (m-40) REVERT: 0 161 LEU cc_start: 0.9066 (tp) cc_final: 0.8621 (tp) REVERT: 2 127 GLN cc_start: 0.8322 (tp40) cc_final: 0.8002 (tp40) REVERT: 4 127 GLN cc_start: 0.7823 (tp40) cc_final: 0.7364 (tp-100) REVERT: 4 131 ASP cc_start: 0.8003 (p0) cc_final: 0.7375 (p0) REVERT: 4 142 ARG cc_start: 0.7949 (mmt-90) cc_final: 0.6758 (mmt90) REVERT: 4 150 PHE cc_start: 0.9075 (p90) cc_final: 0.8573 (p90) REVERT: 6 127 GLN cc_start: 0.8862 (tp40) cc_final: 0.8208 (tp40) REVERT: 6 138 ARG cc_start: 0.8416 (mtp85) cc_final: 0.7443 (mtm110) REVERT: 6 149 THR cc_start: 0.9077 (m) cc_final: 0.8259 (p) REVERT: 6 168 LEU cc_start: 0.8799 (tp) cc_final: 0.8422 (tp) REVERT: 8 144 ASN cc_start: 0.7855 (t0) cc_final: 0.7423 (t0) REVERT: x 149 THR cc_start: 0.9457 (t) cc_final: 0.9224 (p) REVERT: x 150 PHE cc_start: 0.9237 (p90) cc_final: 0.8589 (p90) REVERT: x 153 SER cc_start: 0.9554 (t) cc_final: 0.8999 (p) REVERT: x 168 LEU cc_start: 0.9414 (tp) cc_final: 0.9198 (tt) REVERT: y 115 ILE cc_start: 0.9335 (mt) cc_final: 0.9050 (mt) REVERT: y 158 LEU cc_start: 0.8280 (tp) cc_final: 0.7920 (mm) REVERT: y 160 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7812 (mm-30) REVERT: y 164 ASN cc_start: 0.8730 (m-40) cc_final: 0.8389 (m-40) REVERT: z 127 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8023 (tm-30) REVERT: z 149 THR cc_start: 0.8990 (m) cc_final: 0.8644 (t) REVERT: 1 133 ASN cc_start: 0.8700 (m-40) cc_final: 0.8360 (t0) REVERT: 3 115 ILE cc_start: 0.8899 (mt) cc_final: 0.8610 (mt) REVERT: 5 131 ASP cc_start: 0.8188 (p0) cc_final: 0.7812 (p0) REVERT: 7 168 LEU cc_start: 0.9050 (tp) cc_final: 0.8841 (tp) REVERT: 9 128 TYR cc_start: 0.8839 (t80) cc_final: 0.8595 (t80) REVERT: a 26 LEU cc_start: 0.8910 (tp) cc_final: 0.8587 (tp) REVERT: a 31 THR cc_start: 0.7940 (m) cc_final: 0.7493 (m) REVERT: a 72 LYS cc_start: 0.9627 (tmtt) cc_final: 0.9149 (tptp) REVERT: a 80 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8294 (tm-30) REVERT: b 43 ASN cc_start: 0.7015 (m110) cc_final: 0.6801 (m110) REVERT: b 45 GLN cc_start: 0.8550 (tp40) cc_final: 0.7758 (tm-30) REVERT: b 49 GLU cc_start: 0.7655 (mm-30) cc_final: 0.6950 (mm-30) REVERT: b 65 SER cc_start: 0.9306 (m) cc_final: 0.8887 (t) REVERT: c 59 LEU cc_start: 0.9480 (mt) cc_final: 0.9018 (mt) REVERT: c 80 GLN cc_start: 0.8802 (tp40) cc_final: 0.8307 (tp40) REVERT: d 57 TYR cc_start: 0.9011 (t80) cc_final: 0.8520 (t80) REVERT: d 71 ILE cc_start: 0.8694 (mm) cc_final: 0.8133 (mm) REVERT: d 75 ASP cc_start: 0.8275 (m-30) cc_final: 0.7926 (m-30) REVERT: e 40 ASN cc_start: 0.8426 (p0) cc_final: 0.8172 (p0) REVERT: e 42 SER cc_start: 0.9496 (m) cc_final: 0.9033 (t) REVERT: e 79 ILE cc_start: 0.9396 (tp) cc_final: 0.9152 (tt) REVERT: f 37 LEU cc_start: 0.8642 (tt) cc_final: 0.8282 (tt) REVERT: f 80 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7949 (tm-30) REVERT: g 30 LEU cc_start: 0.9438 (tp) cc_final: 0.9234 (tp) REVERT: g 79 ILE cc_start: 0.9226 (mm) cc_final: 0.8970 (mm) REVERT: h 11 THR cc_start: 0.8114 (m) cc_final: 0.7821 (m) REVERT: h 59 LEU cc_start: 0.9380 (mp) cc_final: 0.9035 (mp) REVERT: i 80 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8087 (tm-30) REVERT: j 14 SER cc_start: 0.9033 (m) cc_final: 0.8678 (p) REVERT: j 80 GLN cc_start: 0.9170 (tp-100) cc_final: 0.8901 (tp-100) REVERT: k 37 LEU cc_start: 0.9022 (tp) cc_final: 0.8716 (tt) REVERT: k 50 TYR cc_start: 0.9314 (t80) cc_final: 0.8920 (t80) REVERT: k 72 LYS cc_start: 0.8932 (tttt) cc_final: 0.8287 (ttmt) REVERT: k 80 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8119 (tp40) REVERT: l 16 SER cc_start: 0.9093 (m) cc_final: 0.8231 (t) REVERT: l 20 ASP cc_start: 0.7518 (m-30) cc_final: 0.7306 (m-30) REVERT: l 25 THR cc_start: 0.8597 (p) cc_final: 0.7751 (p) REVERT: l 45 GLN cc_start: 0.8076 (tp40) cc_final: 0.7545 (tp40) REVERT: l 50 TYR cc_start: 0.9194 (t80) cc_final: 0.8820 (t80) REVERT: l 59 LEU cc_start: 0.9425 (mt) cc_final: 0.9206 (mp) REVERT: m 20 ASP cc_start: 0.7800 (m-30) cc_final: 0.7274 (m-30) REVERT: m 50 TYR cc_start: 0.8763 (t80) cc_final: 0.8501 (t80) REVERT: m 75 ASP cc_start: 0.8276 (m-30) cc_final: 0.7682 (m-30) REVERT: n 3 VAL cc_start: 0.8564 (t) cc_final: 0.8264 (m) REVERT: n 29 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7327 (tm-30) REVERT: n 49 GLU cc_start: 0.7289 (tm-30) cc_final: 0.7014 (tm-30) REVERT: n 53 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8606 (mmtm) REVERT: n 71 ILE cc_start: 0.9380 (mm) cc_final: 0.9160 (mm) REVERT: n 75 ASP cc_start: 0.8410 (m-30) cc_final: 0.8115 (m-30) REVERT: n 80 GLN cc_start: 0.8838 (tm-30) cc_final: 0.7987 (tm-30) REVERT: o 50 TYR cc_start: 0.9309 (t80) cc_final: 0.8712 (t80) REVERT: p 25 THR cc_start: 0.8314 (p) cc_final: 0.7560 (t) REVERT: p 75 ASP cc_start: 0.8646 (m-30) cc_final: 0.8050 (m-30) REVERT: q 32 LEU cc_start: 0.8164 (tp) cc_final: 0.7834 (tp) REVERT: q 36 LYS cc_start: 0.8680 (mttt) cc_final: 0.8403 (mtmt) REVERT: q 50 TYR cc_start: 0.8381 (t80) cc_final: 0.8121 (t80) REVERT: s 7 ASN cc_start: 0.6836 (m-40) cc_final: 0.5794 (p0) REVERT: s 23 THR cc_start: 0.8715 (m) cc_final: 0.8318 (m) REVERT: s 27 GLN cc_start: 0.8441 (mt0) cc_final: 0.7650 (tm-30) REVERT: s 65 SER cc_start: 0.9111 (t) cc_final: 0.8744 (m) REVERT: s 69 LYS cc_start: 0.8654 (tptm) cc_final: 0.7411 (ttmt) REVERT: t 23 THR cc_start: 0.9061 (t) cc_final: 0.8787 (t) REVERT: t 24 GLN cc_start: 0.8628 (tp40) cc_final: 0.8353 (tp40) REVERT: t 26 LEU cc_start: 0.7898 (mt) cc_final: 0.7672 (mt) REVERT: t 29 GLU cc_start: 0.7075 (pt0) cc_final: 0.6851 (tt0) REVERT: t 51 GLN cc_start: 0.8597 (tt0) cc_final: 0.6920 (mm110) REVERT: t 69 LYS cc_start: 0.9254 (tptm) cc_final: 0.8597 (mttt) REVERT: t 72 LYS cc_start: 0.9502 (tmtt) cc_final: 0.9251 (tttp) REVERT: u 30 LEU cc_start: 0.8856 (tp) cc_final: 0.8600 (tt) REVERT: u 46 LEU cc_start: 0.8688 (tp) cc_final: 0.8461 (tp) REVERT: u 69 LYS cc_start: 0.8883 (tptm) cc_final: 0.7505 (ttmt) REVERT: u 82 PHE cc_start: 0.9003 (m-80) cc_final: 0.8498 (m-80) REVERT: v 18 THR cc_start: 0.8264 (m) cc_final: 0.7950 (m) REVERT: v 25 THR cc_start: 0.8250 (p) cc_final: 0.7840 (p) REVERT: v 32 LEU cc_start: 0.9263 (tp) cc_final: 0.8947 (tp) REVERT: v 36 LYS cc_start: 0.8894 (mttt) cc_final: 0.8594 (mttm) REVERT: v 53 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8648 (mmmm) REVERT: v 69 LYS cc_start: 0.9086 (tptm) cc_final: 0.8140 (mttt) REVERT: w 57 TYR cc_start: 0.8936 (t80) cc_final: 0.8499 (t80) REVERT: w 61 ARG cc_start: 0.8372 (mmt180) cc_final: 0.6590 (ttp-170) REVERT: w 69 LYS cc_start: 0.8914 (tppt) cc_final: 0.7363 (tppt) REVERT: a0 103 LYS cc_start: 0.8120 (tttm) cc_final: 0.7023 (tptt) REVERT: d0 103 LYS cc_start: 0.9265 (ttmt) cc_final: 0.7910 (tptt) REVERT: e0 103 LYS cc_start: 0.8355 (ttmt) cc_final: 0.8136 (tttt) REVERT: f0 103 LYS cc_start: 0.9220 (ttmt) cc_final: 0.8313 (tptt) REVERT: g0 103 LYS cc_start: 0.9089 (mtmt) cc_final: 0.7782 (tptt) REVERT: i0 103 LYS cc_start: 0.8969 (tttt) cc_final: 0.8706 (tptt) REVERT: k0 103 LYS cc_start: 0.8868 (ttmm) cc_final: 0.7959 (tptt) REVERT: l0 103 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8222 (tptt) REVERT: m0 103 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8136 (tptt) REVERT: n0 97 SER cc_start: 0.9056 (m) cc_final: 0.8798 (t) REVERT: p0 103 LYS cc_start: 0.8903 (ttpt) cc_final: 0.8122 (tptt) REVERT: p0 105 ARG cc_start: 0.6919 (tmt170) cc_final: 0.6511 (tpt170) REVERT: q0 103 LYS cc_start: 0.9041 (ttmt) cc_final: 0.8326 (tptt) REVERT: r0 102 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8061 (mt-10) REVERT: r0 103 LYS cc_start: 0.8870 (ttmt) cc_final: 0.7596 (tptt) REVERT: t0 103 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8082 (tptt) REVERT: t0 105 ARG cc_start: 0.9208 (ttm110) cc_final: 0.8024 (tpm170) REVERT: u0 103 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8010 (tptt) REVERT: v0 92 THR cc_start: 0.8588 (m) cc_final: 0.8283 (m) REVERT: v0 103 LYS cc_start: 0.9259 (mttt) cc_final: 0.7825 (tptt) REVERT: w0 103 LYS cc_start: 0.8798 (ttmt) cc_final: 0.8292 (tptt) REVERT: x0 103 LYS cc_start: 0.8529 (ttmt) cc_final: 0.7860 (tptt) outliers start: 3 outliers final: 1 residues processed: 2152 average time/residue: 0.5201 time to fit residues: 1892.0039 Evaluate side-chains 1870 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1869 time to evaluate : 5.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 308 optimal weight: 0.0370 chunk 496 optimal weight: 0.8980 chunk 303 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 345 optimal weight: 0.8980 chunk 521 optimal weight: 4.9990 chunk 479 optimal weight: 0.6980 chunk 414 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 320 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 116 GLN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN J 76 HIS K 162 GLN O 44 GLN P 59 ASN R 19 GLN U 80 GLN V 40 ASN Y 144 ASN ** 0 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 137 HIS 4 137 HIS ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 164 ASN ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN f 43 ASN f 51 GLN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 27 GLN m 81 ASN o 24 GLN u 40 ASN v 81 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44858 Z= 0.201 Angle : 0.657 10.133 60890 Z= 0.322 Chirality : 0.041 0.367 7369 Planarity : 0.004 0.078 7620 Dihedral : 4.240 85.032 5953 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.06 % Allowed : 0.40 % Favored : 99.54 % 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: 2.92 (0.12), residues: 5404 helix: 3.00 (0.08), residues: 4154 sheet: 1.12 (0.33), residues: 224 loop : -2.81 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP w 10 HIS 0.008 0.001 HIS F 11 PHE 0.032 0.002 PHE E 155 TYR 0.036 0.001 TYR T 50 ARG 0.008 0.000 ARG X 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10808 Ramachandran restraints generated. 5404 Oldfield, 0 Emsley, 5404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2145 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 2142 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 CYS cc_start: 0.8373 (p) cc_final: 0.7473 (p) REVERT: A 50 MET cc_start: 0.8117 (ttp) cc_final: 0.7855 (ttm) REVERT: A 68 ILE cc_start: 0.9570 (mt) cc_final: 0.9274 (mt) REVERT: A 69 GLU cc_start: 0.7946 (tp30) cc_final: 0.7195 (mm-30) REVERT: A 101 GLN cc_start: 0.8893 (tt0) cc_final: 0.8478 (tm-30) REVERT: A 142 TYR cc_start: 0.9112 (t80) cc_final: 0.8650 (t80) REVERT: A 152 LYS cc_start: 0.9114 (tttt) cc_final: 0.8724 (ttmt) REVERT: A 205 LYS cc_start: 0.9137 (mttt) cc_final: 0.8143 (tttt) REVERT: B 65 LYS cc_start: 0.8555 (tttp) cc_final: 0.8115 (tmtt) REVERT: B 116 GLN cc_start: 0.8877 (tp40) cc_final: 0.8667 (tp40) REVERT: B 190 LYS cc_start: 0.9254 (mtmt) cc_final: 0.8252 (mtmm) REVERT: C 25 THR cc_start: 0.8995 (p) cc_final: 0.8581 (t) REVERT: C 72 TYR cc_start: 0.5831 (t80) cc_final: 0.5335 (m-10) REVERT: C 117 ARG cc_start: 0.8374 (mtt180) cc_final: 0.7836 (tpt170) REVERT: C 146 GLU cc_start: 0.8566 (tp30) cc_final: 0.8252 (mm-30) REVERT: C 152 LYS cc_start: 0.8706 (tttt) cc_final: 0.8485 (tmtt) REVERT: D 6 SER cc_start: 0.8755 (m) cc_final: 0.8037 (p) REVERT: D 156 TYR cc_start: 0.8540 (m-10) cc_final: 0.8182 (m-10) REVERT: E 44 GLN cc_start: 0.8301 (mp10) cc_final: 0.8034 (mp10) REVERT: E 64 MET cc_start: 0.8693 (mmm) cc_final: 0.8095 (mmm) REVERT: F 128 LYS cc_start: 0.8781 (pttt) cc_final: 0.8367 (tmmt) REVERT: F 133 PHE cc_start: 0.9078 (t80) cc_final: 0.8421 (t80) REVERT: F 152 GLN cc_start: 0.8997 (tt0) cc_final: 0.8478 (tp-100) REVERT: F 153 LEU cc_start: 0.9520 (tp) cc_final: 0.9310 (tp) REVERT: F 190 MET cc_start: 0.8924 (mtp) cc_final: 0.8672 (mtp) REVERT: G 52 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8592 (mtmt) REVERT: G 79 MET cc_start: 0.8619 (mmm) cc_final: 0.8159 (mmm) REVERT: H 77 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7627 (tm-30) REVERT: I 60 LEU cc_start: 0.8557 (mt) cc_final: 0.8306 (mt) REVERT: I 69 GLU cc_start: 0.7693 (tp30) cc_final: 0.6542 (tp30) REVERT: J 70 VAL cc_start: 0.9634 (t) cc_final: 0.9428 (p) REVERT: K 132 LYS cc_start: 0.8644 (mmtp) cc_final: 0.8069 (mttt) REVERT: N 33 LYS cc_start: 0.8652 (mmmm) cc_final: 0.8051 (mmtt) REVERT: N 58 LEU cc_start: 0.9201 (mt) cc_final: 0.8893 (mt) REVERT: O 41 THR cc_start: 0.8894 (t) cc_final: 0.8362 (m) REVERT: P 44 GLN cc_start: 0.8109 (tt0) cc_final: 0.7832 (tt0) REVERT: P 56 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7462 (tm-30) REVERT: P 57 SER cc_start: 0.9034 (m) cc_final: 0.8463 (p) REVERT: R 50 GLU cc_start: 0.8149 (tp30) cc_final: 0.7835 (tm-30) REVERT: S 25 THR cc_start: 0.7601 (t) cc_final: 0.7382 (t) REVERT: S 37 LEU cc_start: 0.9030 (tp) cc_final: 0.8721 (tp) REVERT: T 30 LEU cc_start: 0.9036 (tp) cc_final: 0.8804 (tp) REVERT: T 56 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7786 (tt0) REVERT: V 32 LEU cc_start: 0.8683 (mt) cc_final: 0.8329 (tt) REVERT: W 39 LYS cc_start: 0.8208 (mttt) cc_final: 0.7642 (mptt) REVERT: W 43 ASN cc_start: 0.8460 (t0) cc_final: 0.7808 (t0) REVERT: Y 112 SER cc_start: 0.8054 (p) cc_final: 0.7663 (m) REVERT: Y 123 ASN cc_start: 0.8636 (t0) cc_final: 0.8390 (t0) REVERT: Y 127 GLN cc_start: 0.7816 (tm-30) cc_final: 0.7488 (tm-30) REVERT: Y 131 ASP cc_start: 0.7850 (m-30) cc_final: 0.7405 (m-30) REVERT: Z 133 ASN cc_start: 0.9144 (t0) cc_final: 0.8880 (t0) REVERT: 0 133 ASN cc_start: 0.7916 (m-40) cc_final: 0.7642 (m-40) REVERT: 0 161 LEU cc_start: 0.9049 (tp) cc_final: 0.8611 (tp) REVERT: 2 127 GLN cc_start: 0.8433 (tp40) cc_final: 0.8046 (tp40) REVERT: 4 131 ASP cc_start: 0.7996 (p0) cc_final: 0.7384 (p0) REVERT: 4 142 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.6743 (mmt90) REVERT: 4 150 PHE cc_start: 0.9076 (p90) cc_final: 0.8615 (p90) REVERT: 6 127 GLN cc_start: 0.8831 (tp40) cc_final: 0.8201 (tp40) REVERT: 6 138 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7591 (mtm110) REVERT: 6 149 THR cc_start: 0.9049 (m) cc_final: 0.8168 (p) REVERT: 6 168 LEU cc_start: 0.8765 (tp) cc_final: 0.8431 (tp) REVERT: 8 111 ILE cc_start: 0.9333 (mt) cc_final: 0.9112 (mt) REVERT: 8 144 ASN cc_start: 0.7845 (t0) cc_final: 0.7432 (t0) REVERT: x 150 PHE cc_start: 0.9291 (p90) cc_final: 0.8731 (p90) REVERT: x 153 SER cc_start: 0.9520 (t) cc_final: 0.9018 (p) REVERT: x 168 LEU cc_start: 0.9399 (tp) cc_final: 0.9194 (tt) REVERT: y 115 ILE cc_start: 0.9355 (mt) cc_final: 0.8997 (mt) REVERT: y 134 LEU cc_start: 0.9126 (mp) cc_final: 0.8869 (mt) REVERT: y 158 LEU cc_start: 0.8256 (tp) cc_final: 0.7889 (mm) REVERT: y 160 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7789 (mm-30) REVERT: y 164 ASN cc_start: 0.8711 (m-40) cc_final: 0.8388 (m-40) REVERT: z 127 GLN cc_start: 0.8418 (tm-30) cc_final: 0.8034 (tm-30) REVERT: z 149 THR cc_start: 0.8977 (m) cc_final: 0.8626 (t) REVERT: 1 133 ASN cc_start: 0.8620 (m-40) cc_final: 0.8399 (t0) REVERT: 3 115 ILE cc_start: 0.8860 (mt) cc_final: 0.8512 (mt) REVERT: 7 128 TYR cc_start: 0.8967 (t80) cc_final: 0.8609 (t80) REVERT: 7 168 LEU cc_start: 0.9050 (tp) cc_final: 0.8831 (tp) REVERT: 9 128 TYR cc_start: 0.8859 (t80) cc_final: 0.8609 (t80) REVERT: a 26 LEU cc_start: 0.8886 (tp) cc_final: 0.8592 (tp) REVERT: a 31 THR cc_start: 0.7934 (m) cc_final: 0.7513 (m) REVERT: a 72 LYS cc_start: 0.9629 (tmtt) cc_final: 0.9168 (tptp) REVERT: a 80 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8238 (tm-30) REVERT: b 43 ASN cc_start: 0.7006 (m110) cc_final: 0.6778 (m110) REVERT: b 45 GLN cc_start: 0.8684 (tp40) cc_final: 0.8050 (tm-30) REVERT: b 49 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7052 (mm-30) REVERT: b 53 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8859 (mmmt) REVERT: b 59 LEU cc_start: 0.9326 (mp) cc_final: 0.9037 (mp) REVERT: b 65 SER cc_start: 0.9242 (m) cc_final: 0.8894 (t) REVERT: b 81 ASN cc_start: 0.8901 (m-40) cc_final: 0.8698 (m-40) REVERT: c 59 LEU cc_start: 0.9484 (mt) cc_final: 0.9033 (mt) REVERT: c 80 GLN cc_start: 0.8793 (tp40) cc_final: 0.8337 (tp40) REVERT: d 57 TYR cc_start: 0.9012 (t80) cc_final: 0.8550 (t80) REVERT: d 59 LEU cc_start: 0.9291 (mt) cc_final: 0.9020 (mt) REVERT: d 71 ILE cc_start: 0.8646 (mm) cc_final: 0.8088 (mm) REVERT: d 75 ASP cc_start: 0.8275 (m-30) cc_final: 0.7919 (m-30) REVERT: d 80 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7423 (tm-30) REVERT: e 40 ASN cc_start: 0.8427 (p0) cc_final: 0.8148 (p0) REVERT: e 42 SER cc_start: 0.9473 (m) cc_final: 0.9040 (t) REVERT: e 79 ILE cc_start: 0.9445 (tp) cc_final: 0.9227 (tt) REVERT: f 80 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8086 (tm-30) REVERT: g 67 THR cc_start: 0.9356 (t) cc_final: 0.9124 (t) REVERT: g 79 ILE cc_start: 0.9225 (mm) cc_final: 0.8964 (mm) REVERT: h 59 LEU cc_start: 0.9417 (mp) cc_final: 0.8962 (mp) REVERT: i 80 GLN cc_start: 0.8491 (tm-30) cc_final: 0.8082 (tm-30) REVERT: k 37 LEU cc_start: 0.8962 (tp) cc_final: 0.8652 (tt) REVERT: k 50 TYR cc_start: 0.9299 (t80) cc_final: 0.8916 (t80) REVERT: k 60 TYR cc_start: 0.8719 (t80) cc_final: 0.8415 (t80) REVERT: k 72 LYS cc_start: 0.8895 (tttt) cc_final: 0.8577 (ttmt) REVERT: k 80 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8149 (tp40) REVERT: l 16 SER cc_start: 0.9135 (m) cc_final: 0.8244 (t) REVERT: l 20 ASP cc_start: 0.7501 (m-30) cc_final: 0.7272 (m-30) REVERT: l 25 THR cc_start: 0.8685 (p) cc_final: 0.8155 (p) REVERT: l 45 GLN cc_start: 0.8011 (tp40) cc_final: 0.7505 (tp40) REVERT: l 50 TYR cc_start: 0.9203 (t80) cc_final: 0.8848 (t80) REVERT: m 20 ASP cc_start: 0.7764 (m-30) cc_final: 0.7170 (m-30) REVERT: m 50 TYR cc_start: 0.8808 (t80) cc_final: 0.8510 (t80) REVERT: m 75 ASP cc_start: 0.8274 (m-30) cc_final: 0.7695 (m-30) REVERT: n 3 VAL cc_start: 0.8653 (t) cc_final: 0.8334 (m) REVERT: n 49 GLU cc_start: 0.7291 (tm-30) cc_final: 0.7011 (tm-30) REVERT: n 53 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8618 (mmtm) REVERT: n 71 ILE cc_start: 0.9345 (mm) cc_final: 0.9139 (mm) REVERT: n 75 ASP cc_start: 0.8480 (m-30) cc_final: 0.8123 (m-30) REVERT: n 80 GLN cc_start: 0.8806 (tm-30) cc_final: 0.7973 (tm-30) REVERT: o 14 SER cc_start: 0.8631 (t) cc_final: 0.8145 (p) REVERT: o 50 TYR cc_start: 0.9297 (t80) cc_final: 0.8662 (t80) REVERT: p 25 THR cc_start: 0.8277 (p) cc_final: 0.7527 (t) REVERT: p 75 ASP cc_start: 0.8621 (m-30) cc_final: 0.8050 (m-30) REVERT: q 32 LEU cc_start: 0.8078 (tp) cc_final: 0.7725 (tp) REVERT: q 36 LYS cc_start: 0.8661 (mttt) cc_final: 0.8408 (mtmt) REVERT: r 30 LEU cc_start: 0.8997 (tp) cc_final: 0.8457 (tt) REVERT: r 53 LYS cc_start: 0.9416 (ttmm) cc_final: 0.9204 (ttmm) REVERT: s 7 ASN cc_start: 0.6557 (m-40) cc_final: 0.5319 (p0) REVERT: s 23 THR cc_start: 0.8865 (m) cc_final: 0.8457 (m) REVERT: s 27 GLN cc_start: 0.8427 (mt0) cc_final: 0.7635 (tm-30) REVERT: s 65 SER cc_start: 0.9099 (t) cc_final: 0.8742 (m) REVERT: s 69 LYS cc_start: 0.8661 (tptm) cc_final: 0.7429 (ttmt) REVERT: t 29 GLU cc_start: 0.6975 (pt0) cc_final: 0.6658 (tt0) REVERT: t 51 GLN cc_start: 0.8574 (tt0) cc_final: 0.6931 (mm110) REVERT: t 69 LYS cc_start: 0.9278 (tptm) cc_final: 0.8619 (mttt) REVERT: t 72 LYS cc_start: 0.9489 (tmtt) cc_final: 0.9242 (tttp) REVERT: u 30 LEU cc_start: 0.8936 (tp) cc_final: 0.8608 (tt) REVERT: u 65 SER cc_start: 0.9165 (t) cc_final: 0.8929 (t) REVERT: u 69 LYS cc_start: 0.8870 (tptm) cc_final: 0.7535 (ttmt) REVERT: u 82 PHE cc_start: 0.8970 (m-80) cc_final: 0.8433 (m-80) REVERT: v 25 THR cc_start: 0.8230 (p) cc_final: 0.7939 (p) REVERT: v 32 LEU cc_start: 0.9244 (tp) cc_final: 0.8942 (tp) REVERT: v 36 LYS cc_start: 0.8875 (mttt) cc_final: 0.8585 (mttm) REVERT: v 53 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8619 (mmmm) REVERT: v 69 LYS cc_start: 0.9089 (tptm) cc_final: 0.8134 (mttt) REVERT: w 57 TYR cc_start: 0.8944 (t80) cc_final: 0.8494 (t80) REVERT: w 61 ARG cc_start: 0.8267 (mmt180) cc_final: 0.6599 (ttp-170) REVERT: w 69 LYS cc_start: 0.8909 (tppt) cc_final: 0.7413 (tppt) REVERT: a0 103 LYS cc_start: 0.8096 (tttm) cc_final: 0.7004 (tptt) REVERT: d0 103 LYS cc_start: 0.9251 (ttmt) cc_final: 0.7918 (tptt) REVERT: e0 103 LYS cc_start: 0.8724 (ttmt) cc_final: 0.7887 (tttt) REVERT: f0 100 ARG cc_start: 0.8637 (ttm170) cc_final: 0.8422 (ttm170) REVERT: f0 103 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8319 (tptt) REVERT: g0 103 LYS cc_start: 0.9081 (mtmt) cc_final: 0.7808 (tptt) REVERT: i0 103 LYS cc_start: 0.8962 (tttt) cc_final: 0.8701 (tptt) REVERT: k0 103 LYS cc_start: 0.8872 (ttmm) cc_final: 0.7961 (tptt) REVERT: l0 103 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8222 (tptt) REVERT: m0 103 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8130 (tptt) REVERT: p0 103 LYS cc_start: 0.8882 (ttpt) cc_final: 0.8115 (tptt) REVERT: p0 105 ARG cc_start: 0.6903 (tmt170) cc_final: 0.6516 (tpt170) REVERT: q0 103 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8308 (tptt) REVERT: r0 102 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8074 (mt-10) REVERT: r0 103 LYS cc_start: 0.8874 (ttmt) cc_final: 0.7584 (tptt) REVERT: t0 103 LYS cc_start: 0.8880 (ttmt) cc_final: 0.8046 (tptt) REVERT: t0 105 ARG cc_start: 0.9213 (ttm110) cc_final: 0.8022 (tpm170) REVERT: u0 98 SER cc_start: 0.9048 (m) cc_final: 0.8787 (m) REVERT: u0 103 LYS cc_start: 0.9103 (ttmt) cc_final: 0.7998 (tptt) REVERT: v0 92 THR cc_start: 0.8576 (m) cc_final: 0.8286 (m) REVERT: v0 103 LYS cc_start: 0.9242 (mttt) cc_final: 0.7777 (tptt) REVERT: w0 103 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8284 (tptt) REVERT: x0 103 LYS cc_start: 0.8496 (ttmt) cc_final: 0.7852 (tptt) outliers start: 3 outliers final: 1 residues processed: 2143 average time/residue: 0.5132 time to fit residues: 1853.4024 Evaluate side-chains 1860 residues out of total 5011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1859 time to evaluate : 5.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 329 optimal weight: 3.9990 chunk 441 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 382 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 415 optimal weight: 2.9990 chunk 173 optimal weight: 0.5980 chunk 426 optimal weight: 0.7980 chunk 52 optimal weight: 0.0000 chunk 76 optimal weight: 0.7980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN D 116 GLN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 119 ASN F 170 ASN F 247 HIS F 252 ASN J 76 HIS K 162 GLN O 44 GLN P 59 ASN R 19 GLN T 80 GLN U 81 ASN W 81 ASN Y 144 ASN 2 137 HIS 4 137 HIS ** y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 ASN ** c 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 40 ASN f 43 ASN f 51 GLN g 40 ASN g 81 ASN h 66 ASN ** i 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 81 ASN o 24 GLN o 40 ASN t 24 GLN u 40 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102462 restraints weight = 89715.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.105037 restraints weight = 52702.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106802 restraints weight = 35590.214| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44858 Z= 0.198 Angle : 0.660 10.226 60890 Z= 0.322 Chirality : 0.041 0.357 7369 Planarity : 0.004 0.078 7620 Dihedral : 4.222 83.939 5953 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.10 % Allowed : 0.36 % Favored : 99.54 % 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: 2.92 (0.12), residues: 5404 helix: 2.99 (0.08), residues: 4159 sheet: 1.15 (0.32), residues: 224 loop : -2.82 (0.17), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP w 10 HIS 0.008 0.001 HIS F 11 PHE 0.028 0.002 PHE c 19 TYR 0.036 0.001 TYR E 158 ARG 0.015 0.000 ARG K 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23601.48 seconds wall clock time: 418 minutes 29.83 seconds (25109.83 seconds total)