Starting phenix.real_space_refine on Mon Mar 11 01:54:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/03_2024/6i1x_0326_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/03_2024/6i1x_0326.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/03_2024/6i1x_0326.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/03_2024/6i1x_0326.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/03_2024/6i1x_0326_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6i1x_0326/03_2024/6i1x_0326_neut.pdb" } resolution = 3.7 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.009 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 150 5.16 5 C 34155 2.51 5 N 9675 2.21 5 O 10935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 168": "OD1" <-> "OD2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 510": "NH1" <-> "NH2" Residue "A TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 555": "NH1" <-> "NH2" Residue "B ASP 168": "OD1" <-> "OD2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 510": "NH1" <-> "NH2" Residue "B TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 555": "NH1" <-> "NH2" Residue "C ASP 168": "OD1" <-> "OD2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 236": "NH1" <-> "NH2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 510": "NH1" <-> "NH2" Residue "C TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "D ASP 168": "OD1" <-> "OD2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 236": "NH1" <-> "NH2" Residue "D TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 510": "NH1" <-> "NH2" Residue "D TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 555": "NH1" <-> "NH2" Residue "E ASP 168": "OD1" <-> "OD2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 555": "NH1" <-> "NH2" Residue "F ASP 168": "OD1" <-> "OD2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 510": "NH1" <-> "NH2" Residue "F TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 555": "NH1" <-> "NH2" Residue "G ASP 168": "OD1" <-> "OD2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G ARG 236": "NH1" <-> "NH2" Residue "G TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 510": "NH1" <-> "NH2" Residue "G TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 555": "NH1" <-> "NH2" Residue "H ASP 168": "OD1" <-> "OD2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H ARG 236": "NH1" <-> "NH2" Residue "H TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 510": "NH1" <-> "NH2" Residue "H TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 555": "NH1" <-> "NH2" Residue "I ASP 168": "OD1" <-> "OD2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ARG 236": "NH1" <-> "NH2" Residue "I TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 510": "NH1" <-> "NH2" Residue "I TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 555": "NH1" <-> "NH2" Residue "I GLU 616": "OE1" <-> "OE2" Residue "J ASP 168": "OD1" <-> "OD2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J ARG 236": "NH1" <-> "NH2" Residue "J GLU 237": "OE1" <-> "OE2" Residue "J TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 510": "NH1" <-> "NH2" Residue "J TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 555": "NH1" <-> "NH2" Residue "K ASP 168": "OD1" <-> "OD2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K ARG 236": "NH1" <-> "NH2" Residue "K GLU 237": "OE1" <-> "OE2" Residue "K TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 510": "NH1" <-> "NH2" Residue "K TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 555": "NH1" <-> "NH2" Residue "L ASP 168": "OD1" <-> "OD2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 510": "NH1" <-> "NH2" Residue "L TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 555": "NH1" <-> "NH2" Residue "M ASP 168": "OD1" <-> "OD2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ARG 236": "NH1" <-> "NH2" Residue "M TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 510": "NH1" <-> "NH2" Residue "M TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 555": "NH1" <-> "NH2" Residue "N ASP 168": "OD1" <-> "OD2" Residue "N ARG 232": "NH1" <-> "NH2" Residue "N ARG 236": "NH1" <-> "NH2" Residue "N TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 510": "NH1" <-> "NH2" Residue "N TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 555": "NH1" <-> "NH2" Residue "O ASP 168": "OD1" <-> "OD2" Residue "O ARG 232": "NH1" <-> "NH2" Residue "O ARG 236": "NH1" <-> "NH2" Residue "O GLU 237": "OE1" <-> "OE2" Residue "O TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 510": "NH1" <-> "NH2" Residue "O TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 555": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 54915 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "D" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "E" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "F" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "G" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "H" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "I" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "J" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "K" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "L" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "M" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "N" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Chain: "O" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3661 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 16, 'TRANS': 469} Chain breaks: 2 Time building chain proxies: 20.26, per 1000 atoms: 0.37 Number of scatterers: 54915 At special positions: 0 Unit cell: (158.51, 157.3, 182.71, 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 150 16.00 O 10935 8.00 N 9675 7.00 C 34155 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.70 Conformation dependent library (CDL) restraints added in 7.6 seconds 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13290 Finding SS restraints... Secondary structure from input PDB file: 195 helices and 0 sheets defined 32.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.90 Creating SS restraints... Processing helix chain 'A' and resid 111 through 114 removed outlier: 3.723A pdb=" N GLU A 114 " --> pdb=" O SER A 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 115 through 124 Processing helix chain 'A' and resid 145 through 163 removed outlier: 3.888A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.596A pdb=" N GLN A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 266 removed outlier: 3.852A pdb=" N GLU A 259 " --> pdb=" O LYS A 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 263 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 366 through 377 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 549 through 554 Processing helix chain 'A' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N TYR A 605 " --> pdb=" O ALA A 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 removed outlier: 3.729A pdb=" N GLU B 114 " --> pdb=" O SER B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 114' Processing helix chain 'B' and resid 115 through 124 Processing helix chain 'B' and resid 145 through 163 removed outlier: 3.910A pdb=" N GLY B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 186 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 220 through 235 removed outlier: 3.589A pdb=" N GLN B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 266 removed outlier: 3.851A pdb=" N GLU B 259 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 Processing helix chain 'B' and resid 366 through 377 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 549 through 554 Processing helix chain 'B' and resid 578 through 607 removed outlier: 3.658A pdb=" N GLY B 583 " --> pdb=" O ASN B 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 588 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR B 605 " --> pdb=" O ALA B 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 removed outlier: 3.736A pdb=" N GLU C 114 " --> pdb=" O SER C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 115 through 124 Processing helix chain 'C' and resid 145 through 163 removed outlier: 3.896A pdb=" N GLY C 163 " --> pdb=" O VAL C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 220 through 234 removed outlier: 3.590A pdb=" N GLN C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 266 removed outlier: 3.847A pdb=" N GLU C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY C 263 " --> pdb=" O GLU C 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 323 Processing helix chain 'C' and resid 366 through 377 Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 549 through 554 Processing helix chain 'C' and resid 578 through 607 removed outlier: 3.659A pdb=" N GLY C 583 " --> pdb=" O ASN C 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 588 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N TYR C 605 " --> pdb=" O ALA C 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 114 removed outlier: 3.720A pdb=" N GLU D 114 " --> pdb=" O SER D 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 111 through 114' Processing helix chain 'D' and resid 115 through 124 Processing helix chain 'D' and resid 145 through 163 removed outlier: 3.892A pdb=" N GLY D 163 " --> pdb=" O VAL D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 199 through 203 Processing helix chain 'D' and resid 220 through 234 removed outlier: 3.601A pdb=" N GLN D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 266 removed outlier: 3.837A pdb=" N GLU D 259 " --> pdb=" O LYS D 255 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 323 Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 383 through 390 Processing helix chain 'D' and resid 543 through 547 Processing helix chain 'D' and resid 549 through 554 Processing helix chain 'D' and resid 578 through 607 removed outlier: 3.659A pdb=" N GLY D 583 " --> pdb=" O ASN D 579 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS D 588 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 114 removed outlier: 3.725A pdb=" N GLU E 114 " --> pdb=" O SER E 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 111 through 114' Processing helix chain 'E' and resid 115 through 124 Processing helix chain 'E' and resid 145 through 163 removed outlier: 3.887A pdb=" N GLY E 163 " --> pdb=" O VAL E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 186 Processing helix chain 'E' and resid 199 through 203 Processing helix chain 'E' and resid 220 through 234 removed outlier: 3.625A pdb=" N GLN E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 266 removed outlier: 3.805A pdb=" N GLU E 259 " --> pdb=" O LYS E 255 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL E 264 " --> pdb=" O VAL E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 323 Processing helix chain 'E' and resid 366 through 377 Processing helix chain 'E' and resid 383 through 390 Processing helix chain 'E' and resid 543 through 547 Processing helix chain 'E' and resid 549 through 554 Processing helix chain 'E' and resid 578 through 607 removed outlier: 3.644A pdb=" N GLY E 583 " --> pdb=" O ASN E 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS E 588 " --> pdb=" O ILE E 584 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR E 605 " --> pdb=" O ALA E 601 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 114 removed outlier: 3.713A pdb=" N GLU F 114 " --> pdb=" O SER F 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 111 through 114' Processing helix chain 'F' and resid 115 through 124 Processing helix chain 'F' and resid 145 through 163 removed outlier: 3.887A pdb=" N GLY F 163 " --> pdb=" O VAL F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 186 Processing helix chain 'F' and resid 199 through 203 Processing helix chain 'F' and resid 220 through 234 removed outlier: 3.632A pdb=" N GLN F 229 " --> pdb=" O ALA F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 266 removed outlier: 3.822A pdb=" N GLU F 259 " --> pdb=" O LYS F 255 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL F 264 " --> pdb=" O VAL F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 323 Processing helix chain 'F' and resid 366 through 377 Processing helix chain 'F' and resid 383 through 390 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 549 through 554 Processing helix chain 'F' and resid 578 through 607 removed outlier: 3.665A pdb=" N GLY F 583 " --> pdb=" O ASN F 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS F 588 " --> pdb=" O ILE F 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR F 605 " --> pdb=" O ALA F 601 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 114 removed outlier: 3.704A pdb=" N GLU G 114 " --> pdb=" O SER G 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 114' Processing helix chain 'G' and resid 115 through 124 Processing helix chain 'G' and resid 145 through 163 removed outlier: 3.878A pdb=" N GLY G 163 " --> pdb=" O VAL G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 186 Processing helix chain 'G' and resid 199 through 203 Processing helix chain 'G' and resid 220 through 234 removed outlier: 3.644A pdb=" N GLN G 229 " --> pdb=" O ALA G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 266 removed outlier: 3.804A pdb=" N GLU G 259 " --> pdb=" O LYS G 255 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 263 " --> pdb=" O GLU G 259 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL G 264 " --> pdb=" O VAL G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 323 Processing helix chain 'G' and resid 366 through 377 Processing helix chain 'G' and resid 383 through 390 Processing helix chain 'G' and resid 543 through 547 Processing helix chain 'G' and resid 549 through 554 Processing helix chain 'G' and resid 578 through 607 removed outlier: 3.660A pdb=" N GLY G 583 " --> pdb=" O ASN G 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS G 588 " --> pdb=" O ILE G 584 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR G 605 " --> pdb=" O ALA G 601 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 114 removed outlier: 3.713A pdb=" N GLU H 114 " --> pdb=" O SER H 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 114' Processing helix chain 'H' and resid 115 through 124 Processing helix chain 'H' and resid 145 through 163 removed outlier: 3.907A pdb=" N GLY H 163 " --> pdb=" O VAL H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 186 Processing helix chain 'H' and resid 199 through 203 Processing helix chain 'H' and resid 220 through 234 removed outlier: 3.623A pdb=" N GLN H 229 " --> pdb=" O ALA H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 266 removed outlier: 3.840A pdb=" N GLU H 259 " --> pdb=" O LYS H 255 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY H 263 " --> pdb=" O GLU H 259 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL H 264 " --> pdb=" O VAL H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 323 Processing helix chain 'H' and resid 366 through 377 Processing helix chain 'H' and resid 383 through 390 Processing helix chain 'H' and resid 543 through 547 Processing helix chain 'H' and resid 549 through 554 Processing helix chain 'H' and resid 578 through 607 removed outlier: 3.662A pdb=" N GLY H 583 " --> pdb=" O ASN H 579 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 588 " --> pdb=" O ILE H 584 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR H 605 " --> pdb=" O ALA H 601 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 114 removed outlier: 3.758A pdb=" N GLU I 114 " --> pdb=" O SER I 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 111 through 114' Processing helix chain 'I' and resid 115 through 124 Processing helix chain 'I' and resid 145 through 163 removed outlier: 3.863A pdb=" N GLY I 163 " --> pdb=" O VAL I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 220 through 235 removed outlier: 3.637A pdb=" N GLN I 229 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 266 removed outlier: 3.833A pdb=" N GLU I 259 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL I 260 " --> pdb=" O ASP I 256 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY I 263 " --> pdb=" O GLU I 259 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL I 264 " --> pdb=" O VAL I 260 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 323 Processing helix chain 'I' and resid 366 through 377 removed outlier: 3.512A pdb=" N VAL I 370 " --> pdb=" O GLY I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 383 through 390 Processing helix chain 'I' and resid 543 through 547 Processing helix chain 'I' and resid 549 through 554 Processing helix chain 'I' and resid 578 through 607 removed outlier: 3.673A pdb=" N GLY I 583 " --> pdb=" O ASN I 579 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 588 " --> pdb=" O ILE I 584 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR I 605 " --> pdb=" O ALA I 601 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 114 removed outlier: 3.744A pdb=" N GLU J 114 " --> pdb=" O SER J 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 114' Processing helix chain 'J' and resid 115 through 124 Processing helix chain 'J' and resid 145 through 163 removed outlier: 3.897A pdb=" N GLY J 163 " --> pdb=" O VAL J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 199 through 203 Processing helix chain 'J' and resid 220 through 235 removed outlier: 3.587A pdb=" N GLN J 229 " --> pdb=" O ALA J 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 266 removed outlier: 3.845A pdb=" N GLU J 259 " --> pdb=" O LYS J 255 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL J 260 " --> pdb=" O ASP J 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY J 263 " --> pdb=" O GLU J 259 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL J 264 " --> pdb=" O VAL J 260 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 323 Processing helix chain 'J' and resid 366 through 377 Processing helix chain 'J' and resid 383 through 390 Processing helix chain 'J' and resid 543 through 547 Processing helix chain 'J' and resid 549 through 554 Processing helix chain 'J' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY J 583 " --> pdb=" O ASN J 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS J 588 " --> pdb=" O ILE J 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR J 605 " --> pdb=" O ALA J 601 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 114 removed outlier: 3.720A pdb=" N GLU K 114 " --> pdb=" O SER K 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 111 through 114' Processing helix chain 'K' and resid 115 through 124 Processing helix chain 'K' and resid 145 through 163 removed outlier: 3.899A pdb=" N GLY K 163 " --> pdb=" O VAL K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 199 through 203 Processing helix chain 'K' and resid 220 through 234 removed outlier: 3.601A pdb=" N GLN K 229 " --> pdb=" O ALA K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 266 removed outlier: 3.840A pdb=" N GLU K 259 " --> pdb=" O LYS K 255 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL K 260 " --> pdb=" O ASP K 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY K 263 " --> pdb=" O GLU K 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL K 264 " --> pdb=" O VAL K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 323 Processing helix chain 'K' and resid 366 through 377 Processing helix chain 'K' and resid 383 through 390 Processing helix chain 'K' and resid 543 through 547 Processing helix chain 'K' and resid 549 through 554 Processing helix chain 'K' and resid 578 through 607 removed outlier: 3.656A pdb=" N GLY K 583 " --> pdb=" O ASN K 579 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS K 588 " --> pdb=" O ILE K 584 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR K 605 " --> pdb=" O ALA K 601 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 114 removed outlier: 3.729A pdb=" N GLU L 114 " --> pdb=" O SER L 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 111 through 114' Processing helix chain 'L' and resid 115 through 124 Processing helix chain 'L' and resid 145 through 163 removed outlier: 3.901A pdb=" N GLY L 163 " --> pdb=" O VAL L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 199 through 203 Processing helix chain 'L' and resid 220 through 235 removed outlier: 3.594A pdb=" N GLN L 229 " --> pdb=" O ALA L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 253 through 266 removed outlier: 3.845A pdb=" N GLU L 259 " --> pdb=" O LYS L 255 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL L 260 " --> pdb=" O ASP L 256 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY L 263 " --> pdb=" O GLU L 259 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 308 through 323 Processing helix chain 'L' and resid 366 through 377 Processing helix chain 'L' and resid 383 through 390 Processing helix chain 'L' and resid 543 through 547 Processing helix chain 'L' and resid 549 through 554 Processing helix chain 'L' and resid 578 through 607 removed outlier: 3.654A pdb=" N GLY L 583 " --> pdb=" O ASN L 579 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS L 588 " --> pdb=" O ILE L 584 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR L 605 " --> pdb=" O ALA L 601 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 114 removed outlier: 3.735A pdb=" N GLU M 114 " --> pdb=" O SER M 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 111 through 114' Processing helix chain 'M' and resid 115 through 124 Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.903A pdb=" N GLY M 163 " --> pdb=" O VAL M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 186 Processing helix chain 'M' and resid 199 through 203 Processing helix chain 'M' and resid 220 through 235 removed outlier: 3.594A pdb=" N GLN M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 253 through 266 removed outlier: 3.842A pdb=" N GLU M 259 " --> pdb=" O LYS M 255 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL M 260 " --> pdb=" O ASP M 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY M 263 " --> pdb=" O GLU M 259 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL M 264 " --> pdb=" O VAL M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 308 through 323 Processing helix chain 'M' and resid 366 through 377 Processing helix chain 'M' and resid 383 through 390 Processing helix chain 'M' and resid 543 through 547 Processing helix chain 'M' and resid 549 through 554 Processing helix chain 'M' and resid 578 through 607 removed outlier: 3.654A pdb=" N GLY M 583 " --> pdb=" O ASN M 579 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS M 588 " --> pdb=" O ILE M 584 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR M 605 " --> pdb=" O ALA M 601 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 114 removed outlier: 3.722A pdb=" N GLU N 114 " --> pdb=" O SER N 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 111 through 114' Processing helix chain 'N' and resid 115 through 124 Processing helix chain 'N' and resid 145 through 163 removed outlier: 3.895A pdb=" N GLY N 163 " --> pdb=" O VAL N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 186 Processing helix chain 'N' and resid 199 through 203 Processing helix chain 'N' and resid 220 through 234 removed outlier: 3.600A pdb=" N GLN N 229 " --> pdb=" O ALA N 225 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 266 removed outlier: 3.839A pdb=" N GLU N 259 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL N 260 " --> pdb=" O ASP N 256 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY N 263 " --> pdb=" O GLU N 259 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL N 264 " --> pdb=" O VAL N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 308 through 323 Processing helix chain 'N' and resid 366 through 377 Processing helix chain 'N' and resid 383 through 390 Processing helix chain 'N' and resid 543 through 547 Processing helix chain 'N' and resid 549 through 554 Processing helix chain 'N' and resid 578 through 607 removed outlier: 3.657A pdb=" N GLY N 583 " --> pdb=" O ASN N 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS N 588 " --> pdb=" O ILE N 584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR N 605 " --> pdb=" O ALA N 601 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 114 removed outlier: 3.724A pdb=" N GLU O 114 " --> pdb=" O SER O 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 111 through 114' Processing helix chain 'O' and resid 115 through 124 Processing helix chain 'O' and resid 145 through 163 removed outlier: 3.899A pdb=" N GLY O 163 " --> pdb=" O VAL O 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 176 through 186 Processing helix chain 'O' and resid 199 through 203 Processing helix chain 'O' and resid 220 through 234 removed outlier: 3.598A pdb=" N GLN O 229 " --> pdb=" O ALA O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 266 removed outlier: 3.839A pdb=" N GLU O 259 " --> pdb=" O LYS O 255 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL O 260 " --> pdb=" O ASP O 256 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY O 263 " --> pdb=" O GLU O 259 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL O 264 " --> pdb=" O VAL O 260 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 323 Processing helix chain 'O' and resid 366 through 377 Processing helix chain 'O' and resid 383 through 390 Processing helix chain 'O' and resid 543 through 547 Processing helix chain 'O' and resid 549 through 554 Processing helix chain 'O' and resid 578 through 607 removed outlier: 3.655A pdb=" N GLY O 583 " --> pdb=" O ASN O 579 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS O 588 " --> pdb=" O ILE O 584 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR O 605 " --> pdb=" O ALA O 601 " (cutoff:3.500A) 1459 hydrogen bonds defined for protein. 4062 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: 10.62 Time building geometry restraints manager: 17.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 11082 1.32 - 1.45: 11247 1.45 - 1.58: 32856 1.58 - 1.70: 0 1.70 - 1.83: 300 Bond restraints: 55485 Sorted by residual: bond pdb=" CA TYR F 174 " pdb=" C TYR F 174 " ideal model delta sigma weight residual 1.520 1.545 -0.026 4.80e-03 4.34e+04 2.89e+01 bond pdb=" CA TYR G 174 " pdb=" C TYR G 174 " ideal model delta sigma weight residual 1.520 1.544 -0.025 4.80e-03 4.34e+04 2.65e+01 bond pdb=" CA TYR N 174 " pdb=" C TYR N 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.60e+01 bond pdb=" CA TYR K 174 " pdb=" C TYR K 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 bond pdb=" CA TYR D 174 " pdb=" C TYR D 174 " ideal model delta sigma weight residual 1.520 1.544 -0.024 4.80e-03 4.34e+04 2.59e+01 ... (remaining 55480 not shown) Histogram of bond angle deviations from ideal: 94.24 - 102.35: 371 102.35 - 110.45: 13037 110.45 - 118.55: 35793 118.55 - 126.66: 25710 126.66 - 134.76: 344 Bond angle restraints: 75255 Sorted by residual: angle pdb=" N PRO I 609 " pdb=" CA PRO I 609 " pdb=" CB PRO I 609 " ideal model delta sigma weight residual 103.25 94.24 9.01 1.05e+00 9.07e-01 7.36e+01 angle pdb=" N PRO D 609 " pdb=" CA PRO D 609 " pdb=" CB PRO D 609 " ideal model delta sigma weight residual 103.25 94.43 8.82 1.05e+00 9.07e-01 7.06e+01 angle pdb=" N PRO H 609 " pdb=" CA PRO H 609 " pdb=" CB PRO H 609 " ideal model delta sigma weight residual 103.25 94.45 8.80 1.05e+00 9.07e-01 7.03e+01 angle pdb=" N PRO B 609 " pdb=" CA PRO B 609 " pdb=" CB PRO B 609 " ideal model delta sigma weight residual 103.25 94.49 8.76 1.05e+00 9.07e-01 6.96e+01 angle pdb=" N PRO C 609 " pdb=" CA PRO C 609 " pdb=" CB PRO C 609 " ideal model delta sigma weight residual 103.25 94.50 8.75 1.05e+00 9.07e-01 6.94e+01 ... (remaining 75250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 30582 18.10 - 36.19: 2588 36.19 - 54.29: 609 54.29 - 72.39: 121 72.39 - 90.49: 30 Dihedral angle restraints: 33930 sinusoidal: 13230 harmonic: 20700 Sorted by residual: dihedral pdb=" CA LYS I 189 " pdb=" C LYS I 189 " pdb=" N ASP I 190 " pdb=" CA ASP I 190 " ideal model delta harmonic sigma weight residual 180.00 150.09 29.91 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA LYS H 189 " pdb=" C LYS H 189 " pdb=" N ASP H 190 " pdb=" CA ASP H 190 " ideal model delta harmonic sigma weight residual 180.00 151.35 28.65 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA LYS G 189 " pdb=" C LYS G 189 " pdb=" N ASP G 190 " pdb=" CA ASP G 190 " ideal model delta harmonic sigma weight residual 180.00 152.60 27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 33927 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3853 0.061 - 0.123: 3239 0.123 - 0.184: 1572 0.184 - 0.245: 391 0.245 - 0.306: 65 Chirality restraints: 9120 Sorted by residual: chirality pdb=" CA LYS E 250 " pdb=" N LYS E 250 " pdb=" C LYS E 250 " pdb=" CB LYS E 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA LYS F 250 " pdb=" N LYS F 250 " pdb=" C LYS F 250 " pdb=" CB LYS F 250 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA LYS L 250 " pdb=" N LYS L 250 " pdb=" C LYS L 250 " pdb=" CB LYS L 250 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 9117 not shown) Planarity restraints: 9855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 613 " 0.018 2.00e-02 2.50e+03 3.74e-02 1.40e+01 pdb=" C VAL F 613 " -0.065 2.00e-02 2.50e+03 pdb=" O VAL F 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU F 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 613 " 0.018 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C VAL B 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL B 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU B 614 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 613 " 0.017 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C VAL H 613 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL H 613 " 0.025 2.00e-02 2.50e+03 pdb=" N LEU H 614 " 0.022 2.00e-02 2.50e+03 ... (remaining 9852 not shown) Histogram of nonbonded interaction distances: 0.46 - 1.35: 5 1.35 - 2.23: 94 2.23 - 3.12: 45107 3.12 - 4.01: 145267 4.01 - 4.90: 262893 Warning: very small nonbonded interaction distances. Nonbonded interactions: 453366 Sorted by model distance: nonbonded pdb=" CG2 VAL H 139 " pdb=" C ALA I 162 " model vdw 0.458 3.690 nonbonded pdb=" CB VAL H 139 " pdb=" O ALA I 162 " model vdw 0.818 3.470 nonbonded pdb=" CG2 VAL H 139 " pdb=" O ALA I 162 " model vdw 1.091 3.460 nonbonded pdb=" CG2 VAL H 139 " pdb=" N GLY I 163 " model vdw 1.289 3.540 nonbonded pdb=" ND2 ASN I 138 " pdb=" O THR J 198 " model vdw 1.323 2.520 ... (remaining 453361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.450 Check model and map are aligned: 0.600 Set scattering table: 0.400 Process input model: 97.260 Find NCS groups from input model: 3.030 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3237 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 : 0.013 0.061 55485 Z= 0.838 Angle : 1.810 9.397 75255 Z= 1.296 Chirality : 0.098 0.306 9120 Planarity : 0.008 0.072 9855 Dihedral : 14.937 90.487 20640 Min Nonbonded Distance : 0.458 Molprobity Statistics. All-atom Clashscore : 50.06 Ramachandran Plot: Outliers : 1.89 % Allowed : 7.50 % Favored : 90.61 % Rotamer: Outliers : 4.35 % Allowed : 8.17 % Favored : 87.48 % Cbeta Deviations : 0.51 % 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: -3.51 (0.08), residues: 7200 helix: -2.95 (0.08), residues: 1965 sheet: -1.10 (0.10), residues: 2175 loop : -2.72 (0.08), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP I 350 HIS 0.006 0.003 HIS H 133 PHE 0.035 0.007 PHE E 247 TYR 0.039 0.007 TYR H 134 ARG 0.009 0.001 ARG F 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1804 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1541 time to evaluate : 4.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.5898 (t) cc_final: 0.4828 (t) REVERT: A 211 ARG cc_start: 0.4395 (mtt180) cc_final: 0.4192 (ttt180) REVERT: A 229 GLN cc_start: 0.7222 (mt0) cc_final: 0.7018 (mm-40) REVERT: A 255 LYS cc_start: 0.6764 (tttt) cc_final: 0.6536 (mmtt) REVERT: A 259 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5626 (mt-10) REVERT: A 298 GLU cc_start: 0.6169 (tt0) cc_final: 0.5812 (pm20) REVERT: A 312 MET cc_start: 0.7262 (tpp) cc_final: 0.6962 (mmm) REVERT: A 345 ASN cc_start: 0.6678 (p0) cc_final: 0.6193 (p0) REVERT: A 407 MET cc_start: 0.3897 (ttp) cc_final: 0.3218 (tmm) REVERT: A 413 SER cc_start: 0.5500 (m) cc_final: 0.5171 (t) REVERT: A 433 GLU cc_start: 0.6624 (pt0) cc_final: 0.6287 (mt-10) REVERT: A 478 GLU cc_start: 0.7534 (tp30) cc_final: 0.7005 (pp20) REVERT: A 487 GLU cc_start: 0.4338 (tt0) cc_final: 0.4085 (tp30) REVERT: A 534 THR cc_start: 0.7041 (m) cc_final: 0.6302 (m) REVERT: A 550 LEU cc_start: 0.7533 (mt) cc_final: 0.7132 (tp) REVERT: A 553 LEU cc_start: 0.7238 (mt) cc_final: 0.6916 (mt) REVERT: A 558 SER cc_start: 0.3396 (t) cc_final: 0.2744 (m) REVERT: A 560 ASN cc_start: 0.6903 (t0) cc_final: 0.6640 (t0) REVERT: A 591 LEU cc_start: 0.8430 (tp) cc_final: 0.8174 (tp) REVERT: A 602 GLN cc_start: 0.5736 (mt0) cc_final: 0.5511 (tp40) REVERT: B 167 VAL cc_start: 0.6045 (t) cc_final: 0.5403 (t) REVERT: B 174 TYR cc_start: 0.4200 (m-80) cc_final: 0.3920 (m-80) REVERT: B 229 GLN cc_start: 0.6882 (mt0) cc_final: 0.6565 (mm-40) REVERT: B 312 MET cc_start: 0.7779 (tpp) cc_final: 0.7559 (mmm) REVERT: B 345 ASN cc_start: 0.6405 (p0) cc_final: 0.6085 (t0) REVERT: B 359 GLN cc_start: 0.6386 (tt0) cc_final: 0.5970 (tp40) REVERT: B 413 SER cc_start: 0.5064 (m) cc_final: 0.4641 (t) REVERT: B 433 GLU cc_start: 0.6281 (pt0) cc_final: 0.5772 (mp0) REVERT: B 461 ILE cc_start: 0.2494 (OUTLIER) cc_final: 0.2009 (pt) REVERT: B 478 GLU cc_start: 0.7408 (tp30) cc_final: 0.6958 (pp20) REVERT: B 535 LYS cc_start: 0.7736 (ttmt) cc_final: 0.7529 (tttp) REVERT: B 550 LEU cc_start: 0.7398 (mt) cc_final: 0.6814 (tt) REVERT: B 562 SER cc_start: 0.6415 (m) cc_final: 0.6054 (t) REVERT: B 579 ASN cc_start: 0.7270 (m-40) cc_final: 0.6862 (p0) REVERT: B 602 GLN cc_start: 0.7041 (mt0) cc_final: 0.6598 (tp40) REVERT: C 167 VAL cc_start: 0.6930 (t) cc_final: 0.6472 (t) REVERT: C 229 GLN cc_start: 0.7270 (mt0) cc_final: 0.6895 (mm-40) REVERT: C 312 MET cc_start: 0.7687 (tpp) cc_final: 0.7454 (mmm) REVERT: C 325 ARG cc_start: 0.6063 (ttt180) cc_final: 0.5832 (ttm110) REVERT: C 345 ASN cc_start: 0.6445 (p0) cc_final: 0.5918 (t0) REVERT: C 413 SER cc_start: 0.5241 (m) cc_final: 0.4691 (t) REVERT: C 429 MET cc_start: 0.3990 (mmm) cc_final: 0.2918 (mmm) REVERT: C 430 ASP cc_start: 0.3511 (p0) cc_final: 0.2516 (p0) REVERT: C 433 GLU cc_start: 0.6744 (pt0) cc_final: 0.6390 (mt-10) REVERT: C 461 ILE cc_start: 0.2834 (OUTLIER) cc_final: 0.2043 (pt) REVERT: C 463 ARG cc_start: 0.3204 (OUTLIER) cc_final: 0.2888 (mtp85) REVERT: C 503 LEU cc_start: 0.4588 (OUTLIER) cc_final: 0.4262 (mt) REVERT: C 535 LYS cc_start: 0.7612 (ttmt) cc_final: 0.7400 (tttp) REVERT: C 550 LEU cc_start: 0.7228 (mt) cc_final: 0.6808 (tt) REVERT: C 567 MET cc_start: 0.5010 (mmm) cc_final: 0.4806 (mmt) REVERT: C 579 ASN cc_start: 0.7525 (m-40) cc_final: 0.7051 (p0) REVERT: C 591 LEU cc_start: 0.8483 (tp) cc_final: 0.8259 (tp) REVERT: C 602 GLN cc_start: 0.7049 (mt0) cc_final: 0.6784 (tp40) REVERT: D 215 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7461 (p) REVERT: D 227 ILE cc_start: 0.7450 (mt) cc_final: 0.7203 (tp) REVERT: D 229 GLN cc_start: 0.7229 (mt0) cc_final: 0.7000 (mm-40) REVERT: D 259 GLU cc_start: 0.6188 (mm-30) cc_final: 0.5848 (mt-10) REVERT: D 312 MET cc_start: 0.7642 (tpp) cc_final: 0.7439 (mmm) REVERT: D 325 ARG cc_start: 0.6569 (ttt180) cc_final: 0.6263 (ttm170) REVERT: D 345 ASN cc_start: 0.6464 (p0) cc_final: 0.6211 (t0) REVERT: D 433 GLU cc_start: 0.6726 (pt0) cc_final: 0.6417 (mt-10) REVERT: D 463 ARG cc_start: 0.2642 (OUTLIER) cc_final: 0.2344 (mtp85) REVERT: D 475 GLN cc_start: 0.4699 (tt0) cc_final: 0.4286 (tm-30) REVERT: D 535 LYS cc_start: 0.7598 (ttmt) cc_final: 0.7352 (tttp) REVERT: D 550 LEU cc_start: 0.7339 (mt) cc_final: 0.6915 (tt) REVERT: D 562 SER cc_start: 0.6220 (m) cc_final: 0.5860 (t) REVERT: D 579 ASN cc_start: 0.7226 (m-40) cc_final: 0.6804 (p0) REVERT: D 602 GLN cc_start: 0.6813 (mt0) cc_final: 0.6566 (tp40) REVERT: E 190 ASP cc_start: -0.2286 (OUTLIER) cc_final: -0.3142 (m-30) REVERT: E 227 ILE cc_start: 0.7592 (mt) cc_final: 0.7298 (mm) REVERT: E 238 LEU cc_start: 0.5259 (OUTLIER) cc_final: 0.4930 (tp) REVERT: E 246 VAL cc_start: 0.7019 (t) cc_final: 0.6588 (p) REVERT: E 345 ASN cc_start: 0.6552 (p0) cc_final: 0.6330 (p0) REVERT: E 413 SER cc_start: 0.5873 (m) cc_final: 0.5558 (t) REVERT: E 433 GLU cc_start: 0.6246 (pt0) cc_final: 0.6013 (mt-10) REVERT: E 461 ILE cc_start: 0.3244 (OUTLIER) cc_final: 0.2368 (pt) REVERT: E 478 GLU cc_start: 0.7186 (tp30) cc_final: 0.6794 (pp20) REVERT: E 503 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4020 (mt) REVERT: E 534 THR cc_start: 0.7699 (m) cc_final: 0.7352 (m) REVERT: E 535 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7327 (tttp) REVERT: E 579 ASN cc_start: 0.7110 (m-40) cc_final: 0.6801 (p0) REVERT: F 160 ASP cc_start: 0.6044 (t70) cc_final: 0.5828 (m-30) REVERT: F 174 TYR cc_start: 0.4414 (m-80) cc_final: 0.4160 (m-80) REVERT: F 215 VAL cc_start: 0.6449 (OUTLIER) cc_final: 0.6173 (p) REVERT: F 232 ARG cc_start: 0.8457 (mtt180) cc_final: 0.8177 (ptm-80) REVERT: F 244 THR cc_start: 0.6402 (m) cc_final: 0.6109 (m) REVERT: F 312 MET cc_start: 0.6542 (tpp) cc_final: 0.5845 (mmm) REVERT: F 365 PRO cc_start: 0.8019 (Cg_endo) cc_final: 0.7673 (Cg_exo) REVERT: F 433 GLU cc_start: 0.6266 (pt0) cc_final: 0.5896 (mt-10) REVERT: F 461 ILE cc_start: 0.3277 (OUTLIER) cc_final: 0.2646 (pt) REVERT: F 463 ARG cc_start: 0.2380 (OUTLIER) cc_final: 0.1961 (mtp85) REVERT: F 503 LEU cc_start: 0.4888 (OUTLIER) cc_final: 0.4551 (mt) REVERT: F 530 MET cc_start: 0.3772 (mtm) cc_final: 0.3548 (mtt) REVERT: F 535 LYS cc_start: 0.7536 (ttmt) cc_final: 0.7331 (tttp) REVERT: F 553 LEU cc_start: 0.7386 (mt) cc_final: 0.7155 (mp) REVERT: G 160 ASP cc_start: 0.6146 (t70) cc_final: 0.5686 (m-30) REVERT: G 215 VAL cc_start: 0.6304 (OUTLIER) cc_final: 0.6000 (p) REVERT: G 232 ARG cc_start: 0.8489 (mtt180) cc_final: 0.8234 (mtm110) REVERT: G 241 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.6558 (pm20) REVERT: G 246 VAL cc_start: 0.6866 (t) cc_final: 0.6475 (p) REVERT: G 255 LYS cc_start: 0.6839 (tttt) cc_final: 0.6551 (tppt) REVERT: G 365 PRO cc_start: 0.7539 (Cg_endo) cc_final: 0.7238 (Cg_exo) REVERT: G 433 GLU cc_start: 0.6087 (pt0) cc_final: 0.5763 (mt-10) REVERT: G 461 ILE cc_start: 0.3359 (OUTLIER) cc_final: 0.3068 (pt) REVERT: G 463 ARG cc_start: 0.1653 (OUTLIER) cc_final: 0.1412 (mtp85) REVERT: G 535 LYS cc_start: 0.7806 (ttmt) cc_final: 0.7561 (tttp) REVERT: G 550 LEU cc_start: 0.7057 (mt) cc_final: 0.6780 (mt) REVERT: G 562 SER cc_start: 0.6525 (m) cc_final: 0.6267 (t) REVERT: G 579 ASN cc_start: 0.6898 (m-40) cc_final: 0.6368 (p0) REVERT: G 591 LEU cc_start: 0.8086 (tp) cc_final: 0.7803 (tp) REVERT: H 167 VAL cc_start: 0.6822 (t) cc_final: 0.5424 (t) REVERT: H 215 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7363 (p) REVERT: H 227 ILE cc_start: 0.7517 (mt) cc_final: 0.7175 (mm) REVERT: H 230 MET cc_start: 0.7314 (mtp) cc_final: 0.7102 (tmm) REVERT: H 255 LYS cc_start: 0.6555 (tttt) cc_final: 0.6343 (tppt) REVERT: H 316 GLU cc_start: 0.7936 (tt0) cc_final: 0.7455 (tm-30) REVERT: H 325 ARG cc_start: 0.6595 (ttt180) cc_final: 0.6372 (ttt-90) REVERT: H 345 ASN cc_start: 0.7034 (p0) cc_final: 0.6742 (p0) REVERT: H 407 MET cc_start: 0.5008 (ttp) cc_final: 0.4681 (tmm) REVERT: H 413 SER cc_start: 0.5764 (m) cc_final: 0.5407 (p) REVERT: H 433 GLU cc_start: 0.6432 (pt0) cc_final: 0.6066 (mt-10) REVERT: H 461 ILE cc_start: 0.2519 (OUTLIER) cc_final: 0.1907 (pt) REVERT: H 509 THR cc_start: 0.4432 (p) cc_final: 0.4186 (p) REVERT: H 530 MET cc_start: 0.4488 (mtm) cc_final: 0.4226 (mtt) REVERT: H 535 LYS cc_start: 0.7667 (ttmt) cc_final: 0.7358 (tttp) REVERT: H 550 LEU cc_start: 0.7448 (mt) cc_final: 0.7078 (tt) REVERT: H 562 SER cc_start: 0.6484 (m) cc_final: 0.6134 (t) REVERT: H 567 MET cc_start: 0.4725 (mmm) cc_final: 0.4348 (mmt) REVERT: H 579 ASN cc_start: 0.7262 (m-40) cc_final: 0.6751 (p0) REVERT: I 180 MET cc_start: 0.5274 (mmm) cc_final: 0.5024 (mmp) REVERT: I 183 LEU cc_start: 0.6531 (mt) cc_final: 0.6275 (mt) REVERT: I 249 LEU cc_start: 0.5364 (mt) cc_final: 0.4381 (mp) REVERT: I 298 GLU cc_start: 0.7114 (tt0) cc_final: 0.6774 (pt0) REVERT: I 345 ASN cc_start: 0.6918 (p0) cc_final: 0.6691 (t0) REVERT: I 433 GLU cc_start: 0.6445 (pt0) cc_final: 0.6127 (mt-10) REVERT: I 463 ARG cc_start: 0.2832 (OUTLIER) cc_final: 0.2521 (mmm160) REVERT: I 478 GLU cc_start: 0.7549 (tp30) cc_final: 0.7241 (pp20) REVERT: I 480 ASP cc_start: 0.5224 (OUTLIER) cc_final: 0.5010 (p0) REVERT: I 534 THR cc_start: 0.7569 (m) cc_final: 0.7336 (m) REVERT: I 562 SER cc_start: 0.6426 (m) cc_final: 0.6132 (t) REVERT: J 180 MET cc_start: 0.4405 (mmm) cc_final: 0.4187 (mmm) REVERT: J 229 GLN cc_start: 0.7156 (mt0) cc_final: 0.6785 (mm-40) REVERT: J 236 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7992 (mmm160) REVERT: J 259 GLU cc_start: 0.5913 (mm-30) cc_final: 0.5404 (mt-10) REVERT: J 326 ARG cc_start: 0.4557 (mtm-85) cc_final: 0.4311 (mtm110) REVERT: J 345 ASN cc_start: 0.7023 (p0) cc_final: 0.6607 (t0) REVERT: J 413 SER cc_start: 0.5659 (m) cc_final: 0.5153 (t) REVERT: J 424 PRO cc_start: 0.7689 (Cg_endo) cc_final: 0.7414 (Cg_exo) REVERT: J 433 GLU cc_start: 0.6775 (pt0) cc_final: 0.6439 (mt-10) REVERT: J 461 ILE cc_start: 0.2793 (OUTLIER) cc_final: 0.2220 (pt) REVERT: J 463 ARG cc_start: 0.2679 (OUTLIER) cc_final: 0.2436 (mtp85) REVERT: J 478 GLU cc_start: 0.7706 (tp30) cc_final: 0.7266 (pp20) REVERT: J 503 LEU cc_start: 0.4663 (OUTLIER) cc_final: 0.4320 (mt) REVERT: J 550 LEU cc_start: 0.7299 (mt) cc_final: 0.6907 (tt) REVERT: J 562 SER cc_start: 0.6789 (m) cc_final: 0.6300 (t) REVERT: J 579 ASN cc_start: 0.7080 (m-40) cc_final: 0.6569 (p0) REVERT: J 602 GLN cc_start: 0.6679 (mt0) cc_final: 0.6398 (tp40) REVERT: K 168 ASP cc_start: 0.5282 (m-30) cc_final: 0.5066 (p0) REVERT: K 211 ARG cc_start: 0.5337 (mtt180) cc_final: 0.5095 (mtp85) REVERT: K 227 ILE cc_start: 0.7272 (mt) cc_final: 0.6895 (mm) REVERT: K 259 GLU cc_start: 0.6281 (mm-30) cc_final: 0.5883 (mt-10) REVERT: K 312 MET cc_start: 0.7296 (tpp) cc_final: 0.6958 (mmm) REVERT: K 316 GLU cc_start: 0.8078 (tt0) cc_final: 0.7621 (tm-30) REVERT: K 430 ASP cc_start: 0.3201 (p0) cc_final: 0.2840 (p0) REVERT: K 433 GLU cc_start: 0.6683 (pt0) cc_final: 0.6419 (mt-10) REVERT: K 461 ILE cc_start: 0.2511 (OUTLIER) cc_final: 0.2010 (pt) REVERT: K 463 ARG cc_start: 0.2219 (OUTLIER) cc_final: 0.1808 (mtp85) REVERT: K 535 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7304 (tttm) REVERT: K 550 LEU cc_start: 0.7070 (mt) cc_final: 0.6692 (tt) REVERT: K 562 SER cc_start: 0.6848 (m) cc_final: 0.6424 (t) REVERT: K 567 MET cc_start: 0.5183 (mmm) cc_final: 0.4786 (mmm) REVERT: K 579 ASN cc_start: 0.7070 (m-40) cc_final: 0.6594 (p0) REVERT: L 174 TYR cc_start: 0.4523 (m-80) cc_final: 0.4297 (m-80) REVERT: L 229 GLN cc_start: 0.6929 (mt0) cc_final: 0.6610 (mm-40) REVERT: L 312 MET cc_start: 0.7488 (tpp) cc_final: 0.7225 (mmm) REVERT: L 345 ASN cc_start: 0.6745 (p0) cc_final: 0.6417 (t0) REVERT: L 359 GLN cc_start: 0.5251 (tt0) cc_final: 0.4977 (tp40) REVERT: L 413 SER cc_start: 0.5657 (m) cc_final: 0.5201 (t) REVERT: L 433 GLU cc_start: 0.6859 (pt0) cc_final: 0.6619 (mt-10) REVERT: L 461 ILE cc_start: 0.3046 (OUTLIER) cc_final: 0.2558 (pt) REVERT: L 463 ARG cc_start: 0.3109 (OUTLIER) cc_final: 0.2684 (mtp85) REVERT: L 478 GLU cc_start: 0.7772 (tp30) cc_final: 0.7333 (pp20) REVERT: L 534 THR cc_start: 0.7717 (m) cc_final: 0.7491 (m) REVERT: L 550 LEU cc_start: 0.7405 (mt) cc_final: 0.7025 (tt) REVERT: L 562 SER cc_start: 0.6657 (m) cc_final: 0.6301 (t) REVERT: L 579 ASN cc_start: 0.7154 (m-40) cc_final: 0.6776 (p0) REVERT: L 602 GLN cc_start: 0.6719 (mt0) cc_final: 0.6459 (tp40) REVERT: M 174 TYR cc_start: 0.4053 (m-80) cc_final: 0.3815 (m-80) REVERT: M 229 GLN cc_start: 0.6989 (mt0) cc_final: 0.6706 (mm-40) REVERT: M 325 ARG cc_start: 0.6651 (ttt180) cc_final: 0.6295 (tmt170) REVERT: M 345 ASN cc_start: 0.6900 (p0) cc_final: 0.6606 (t0) REVERT: M 359 GLN cc_start: 0.6013 (tt0) cc_final: 0.5623 (tp40) REVERT: M 413 SER cc_start: 0.5078 (m) cc_final: 0.4595 (t) REVERT: M 430 ASP cc_start: 0.3483 (p0) cc_final: 0.3174 (p0) REVERT: M 433 GLU cc_start: 0.6542 (pt0) cc_final: 0.6191 (mt-10) REVERT: M 461 ILE cc_start: 0.2910 (OUTLIER) cc_final: 0.2498 (pt) REVERT: M 463 ARG cc_start: 0.3010 (OUTLIER) cc_final: 0.2504 (mtp85) REVERT: M 475 GLN cc_start: 0.4524 (tt0) cc_final: 0.4267 (tm-30) REVERT: M 478 GLU cc_start: 0.7667 (tp30) cc_final: 0.7227 (pp20) REVERT: M 550 LEU cc_start: 0.7261 (mt) cc_final: 0.6846 (tt) REVERT: M 562 SER cc_start: 0.6636 (m) cc_final: 0.6264 (t) REVERT: M 579 ASN cc_start: 0.6789 (m-40) cc_final: 0.6272 (p0) REVERT: M 602 GLN cc_start: 0.6639 (mt0) cc_final: 0.6398 (tp40) REVERT: M 613 VAL cc_start: 0.4758 (p) cc_final: 0.4542 (t) REVERT: N 227 ILE cc_start: 0.7457 (mt) cc_final: 0.7206 (mm) REVERT: N 229 GLN cc_start: 0.6994 (mt0) cc_final: 0.6661 (mm-40) REVERT: N 259 GLU cc_start: 0.5829 (mm-30) cc_final: 0.5528 (mt-10) REVERT: N 312 MET cc_start: 0.7468 (tpp) cc_final: 0.7090 (mmm) REVERT: N 345 ASN cc_start: 0.6314 (p0) cc_final: 0.5954 (t0) REVERT: N 359 GLN cc_start: 0.5930 (tt0) cc_final: 0.5524 (tp40) REVERT: N 407 MET cc_start: 0.4538 (ttp) cc_final: 0.4026 (tmm) REVERT: N 413 SER cc_start: 0.5514 (m) cc_final: 0.5042 (t) REVERT: N 424 PRO cc_start: 0.7646 (Cg_endo) cc_final: 0.7347 (Cg_exo) REVERT: N 433 GLU cc_start: 0.6114 (pt0) cc_final: 0.5806 (mt-10) REVERT: N 461 ILE cc_start: 0.2520 (OUTLIER) cc_final: 0.1944 (pt) REVERT: N 463 ARG cc_start: 0.2526 (OUTLIER) cc_final: 0.2231 (mtp85) REVERT: N 478 GLU cc_start: 0.7427 (tp30) cc_final: 0.7062 (pp20) REVERT: N 550 LEU cc_start: 0.7259 (mt) cc_final: 0.6838 (tt) REVERT: N 553 LEU cc_start: 0.7418 (mt) cc_final: 0.7206 (mt) REVERT: N 562 SER cc_start: 0.6543 (m) cc_final: 0.5930 (t) REVERT: N 579 ASN cc_start: 0.6941 (m-40) cc_final: 0.6415 (p0) REVERT: O 167 VAL cc_start: 0.6953 (t) cc_final: 0.6442 (t) REVERT: O 174 TYR cc_start: 0.4429 (m-80) cc_final: 0.4172 (m-80) REVERT: O 227 ILE cc_start: 0.7338 (mt) cc_final: 0.7130 (mm) REVERT: O 259 GLU cc_start: 0.5966 (mm-30) cc_final: 0.5514 (mt-10) REVERT: O 298 GLU cc_start: 0.5711 (tt0) cc_final: 0.5471 (mt-10) REVERT: O 312 MET cc_start: 0.7650 (tpp) cc_final: 0.7320 (mmm) REVERT: O 413 SER cc_start: 0.5145 (m) cc_final: 0.4690 (t) REVERT: O 430 ASP cc_start: 0.3187 (p0) cc_final: 0.2769 (p0) REVERT: O 433 GLU cc_start: 0.6340 (pt0) cc_final: 0.6031 (mt-10) REVERT: O 463 ARG cc_start: 0.2364 (OUTLIER) cc_final: 0.2004 (mtp85) REVERT: O 478 GLU cc_start: 0.7568 (tp30) cc_final: 0.7188 (pp20) REVERT: O 534 THR cc_start: 0.7487 (m) cc_final: 0.7279 (m) REVERT: O 535 LYS cc_start: 0.7640 (ttmt) cc_final: 0.7426 (tttp) REVERT: O 550 LEU cc_start: 0.7099 (mt) cc_final: 0.6578 (tt) REVERT: O 554 PHE cc_start: 0.7057 (m-80) cc_final: 0.6852 (m-80) REVERT: O 562 SER cc_start: 0.6826 (m) cc_final: 0.6391 (t) REVERT: O 579 ASN cc_start: 0.7201 (m-40) cc_final: 0.6753 (p0) REVERT: O 591 LEU cc_start: 0.8327 (tp) cc_final: 0.8062 (tp) REVERT: O 602 GLN cc_start: 0.7117 (mt0) cc_final: 0.6903 (tp-100) outliers start: 263 outliers final: 71 residues processed: 1752 average time/residue: 0.5494 time to fit residues: 1564.0175 Evaluate side-chains 932 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 827 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 503 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 238 LEU Chi-restraints excluded: chain E residue 349 GLN Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 482 VAL Chi-restraints excluded: chain E residue 492 SER Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 420 ILE Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 482 VAL Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 241 GLN Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 420 ILE Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 463 ARG Chi-restraints excluded: chain G residue 482 VAL Chi-restraints excluded: chain G residue 492 SER Chi-restraints excluded: chain G residue 503 LEU Chi-restraints excluded: chain H residue 215 VAL Chi-restraints excluded: chain H residue 420 ILE Chi-restraints excluded: chain H residue 461 ILE Chi-restraints excluded: chain H residue 482 VAL Chi-restraints excluded: chain H residue 492 SER Chi-restraints excluded: chain H residue 503 LEU Chi-restraints excluded: chain I residue 305 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 463 ARG Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain I residue 482 VAL Chi-restraints excluded: chain I residue 492 SER Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 241 GLN Chi-restraints excluded: chain J residue 420 ILE Chi-restraints excluded: chain J residue 461 ILE Chi-restraints excluded: chain J residue 463 ARG Chi-restraints excluded: chain J residue 482 VAL Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 420 ILE Chi-restraints excluded: chain K residue 461 ILE Chi-restraints excluded: chain K residue 463 ARG Chi-restraints excluded: chain K residue 482 VAL Chi-restraints excluded: chain K residue 492 SER Chi-restraints excluded: chain K residue 503 LEU Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 461 ILE Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 482 VAL Chi-restraints excluded: chain L residue 492 SER Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 593 ARG Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain M residue 305 ILE Chi-restraints excluded: chain M residue 420 ILE Chi-restraints excluded: chain M residue 461 ILE Chi-restraints excluded: chain M residue 463 ARG Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 492 SER Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain N residue 190 ASP Chi-restraints excluded: chain N residue 305 ILE Chi-restraints excluded: chain N residue 420 ILE Chi-restraints excluded: chain N residue 461 ILE Chi-restraints excluded: chain N residue 463 ARG Chi-restraints excluded: chain N residue 482 VAL Chi-restraints excluded: chain N residue 492 SER Chi-restraints excluded: chain N residue 503 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 305 ILE Chi-restraints excluded: chain O residue 420 ILE Chi-restraints excluded: chain O residue 463 ARG Chi-restraints excluded: chain O residue 482 VAL Chi-restraints excluded: chain O residue 492 SER Chi-restraints excluded: chain O residue 503 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 607 optimal weight: 4.9990 chunk 545 optimal weight: 0.9990 chunk 302 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 368 optimal weight: 0.6980 chunk 291 optimal weight: 7.9990 chunk 564 optimal weight: 2.9990 chunk 218 optimal weight: 0.3980 chunk 343 optimal weight: 0.0050 chunk 420 optimal weight: 6.9990 chunk 653 optimal weight: 6.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 188 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 GLN A 496 GLN ** A 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 404 ASN C 440 GLN ** C 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 ASN F 188 ASN ** F 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 ASN G 233 GLN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 188 ASN ** H 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 188 ASN I 328 GLN I 359 GLN I 440 GLN ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 440 GLN ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 GLN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 188 ASN L 233 GLN ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 349 GLN ** L 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 ASN ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 349 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 186 ASN ** N 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 440 GLN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 ASN O 188 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 349 GLN O 440 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3249 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 55485 Z= 0.261 Angle : 0.815 12.145 75255 Z= 0.419 Chirality : 0.050 0.798 9120 Planarity : 0.006 0.123 9855 Dihedral : 8.682 59.876 7990 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.79 % Favored : 95.79 % Rotamer: Outliers : 4.55 % Allowed : 15.19 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -2.14 (0.09), residues: 7200 helix: -0.85 (0.10), residues: 1935 sheet: -1.12 (0.09), residues: 2730 loop : -1.98 (0.10), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 350 HIS 0.009 0.001 HIS H 133 PHE 0.016 0.002 PHE I 393 TYR 0.034 0.003 TYR H 134 ARG 0.013 0.001 ARG M 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1003 time to evaluate : 5.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: -0.1088 (ttt) cc_final: -0.1759 (mmt) REVERT: A 345 ASN cc_start: 0.6139 (p0) cc_final: 0.5433 (t0) REVERT: A 365 PRO cc_start: 0.7496 (Cg_endo) cc_final: 0.7039 (Cg_exo) REVERT: A 407 MET cc_start: 0.3890 (ttp) cc_final: 0.3488 (tmm) REVERT: A 413 SER cc_start: 0.5370 (m) cc_final: 0.4797 (t) REVERT: A 433 GLU cc_start: 0.6801 (pt0) cc_final: 0.6283 (mp0) REVERT: A 478 GLU cc_start: 0.7436 (tp30) cc_final: 0.6728 (pp20) REVERT: A 512 VAL cc_start: 0.3488 (OUTLIER) cc_final: 0.3202 (p) REVERT: B 100 MET cc_start: -0.1014 (ttt) cc_final: -0.1781 (mmt) REVERT: B 180 MET cc_start: 0.6669 (mmt) cc_final: 0.6253 (mmm) REVERT: B 211 ARG cc_start: 0.5606 (mtt180) cc_final: 0.5227 (ptm160) REVERT: B 345 ASN cc_start: 0.6280 (p0) cc_final: 0.5804 (t0) REVERT: B 433 GLU cc_start: 0.6687 (pt0) cc_final: 0.6141 (mp0) REVERT: B 478 GLU cc_start: 0.7114 (tp30) cc_final: 0.6586 (pp20) REVERT: B 536 GLU cc_start: 0.6008 (tm-30) cc_final: 0.5421 (mp0) REVERT: B 550 LEU cc_start: 0.7087 (mt) cc_final: 0.6866 (tp) REVERT: B 579 ASN cc_start: 0.7406 (m-40) cc_final: 0.7072 (p0) REVERT: B 602 GLN cc_start: 0.6977 (mt0) cc_final: 0.6713 (tp40) REVERT: C 174 TYR cc_start: 0.3505 (m-80) cc_final: 0.3297 (m-80) REVERT: C 211 ARG cc_start: 0.5767 (ttt180) cc_final: 0.5192 (ptm160) REVERT: C 297 ASP cc_start: 0.5076 (t0) cc_final: 0.4248 (t0) REVERT: C 298 GLU cc_start: 0.5971 (mm-30) cc_final: 0.5602 (mt-10) REVERT: C 345 ASN cc_start: 0.6581 (p0) cc_final: 0.6151 (t0) REVERT: C 365 PRO cc_start: 0.7507 (Cg_endo) cc_final: 0.7080 (Cg_exo) REVERT: C 429 MET cc_start: 0.5518 (mmm) cc_final: 0.5167 (mmm) REVERT: C 433 GLU cc_start: 0.6803 (pt0) cc_final: 0.6502 (tt0) REVERT: C 478 GLU cc_start: 0.7202 (tp30) cc_final: 0.6690 (pp20) REVERT: C 550 LEU cc_start: 0.7143 (mt) cc_final: 0.6828 (tp) REVERT: C 579 ASN cc_start: 0.7521 (m-40) cc_final: 0.7086 (p0) REVERT: D 312 MET cc_start: 0.7783 (tpp) cc_final: 0.7523 (mmm) REVERT: D 342 ASP cc_start: 0.6436 (OUTLIER) cc_final: 0.6228 (p0) REVERT: D 345 ASN cc_start: 0.6663 (p0) cc_final: 0.6347 (t0) REVERT: D 365 PRO cc_start: 0.7404 (Cg_endo) cc_final: 0.7039 (Cg_exo) REVERT: D 433 GLU cc_start: 0.6604 (pt0) cc_final: 0.6317 (tt0) REVERT: D 536 GLU cc_start: 0.5947 (tm-30) cc_final: 0.5709 (tm-30) REVERT: D 550 LEU cc_start: 0.6766 (mt) cc_final: 0.6492 (tp) REVERT: E 180 MET cc_start: 0.6801 (mmm) cc_final: 0.6178 (mmm) REVERT: E 316 GLU cc_start: 0.7738 (tt0) cc_final: 0.7320 (tm-30) REVERT: E 433 GLU cc_start: 0.6066 (pt0) cc_final: 0.5771 (mt-10) REVERT: E 461 ILE cc_start: 0.3194 (OUTLIER) cc_final: 0.2895 (pt) REVERT: E 478 GLU cc_start: 0.7096 (tp30) cc_final: 0.6608 (pp20) REVERT: E 595 GLN cc_start: 0.7340 (mt0) cc_final: 0.7139 (mt0) REVERT: F 312 MET cc_start: 0.6542 (tpp) cc_final: 0.5945 (mmm) REVERT: F 433 GLU cc_start: 0.7028 (pt0) cc_final: 0.6736 (tt0) REVERT: F 461 ILE cc_start: 0.3133 (OUTLIER) cc_final: 0.2891 (pt) REVERT: F 535 LYS cc_start: 0.7437 (ttmt) cc_final: 0.7224 (tttp) REVERT: G 215 VAL cc_start: 0.6658 (OUTLIER) cc_final: 0.6449 (p) REVERT: G 230 MET cc_start: 0.6436 (mmp) cc_final: 0.6204 (tmm) REVERT: G 433 GLU cc_start: 0.6942 (pt0) cc_final: 0.6588 (mt-10) REVERT: G 461 ILE cc_start: 0.2277 (OUTLIER) cc_final: 0.2004 (pt) REVERT: G 535 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7472 (tttp) REVERT: G 550 LEU cc_start: 0.6881 (mt) cc_final: 0.6601 (tp) REVERT: H 251 TYR cc_start: 0.5929 (m-80) cc_final: 0.5618 (m-80) REVERT: H 316 GLU cc_start: 0.7782 (tt0) cc_final: 0.7339 (tm-30) REVERT: H 345 ASN cc_start: 0.6353 (p0) cc_final: 0.6065 (t0) REVERT: H 365 PRO cc_start: 0.7772 (Cg_endo) cc_final: 0.7496 (Cg_exo) REVERT: H 407 MET cc_start: 0.5051 (ttp) cc_final: 0.4531 (tmm) REVERT: H 433 GLU cc_start: 0.6873 (pt0) cc_final: 0.6502 (mt-10) REVERT: H 478 GLU cc_start: 0.7596 (tp30) cc_final: 0.6889 (pp20) REVERT: I 433 GLU cc_start: 0.6509 (pt0) cc_final: 0.6239 (tt0) REVERT: I 478 GLU cc_start: 0.7356 (tp30) cc_final: 0.6930 (pt0) REVERT: I 480 ASP cc_start: 0.5334 (OUTLIER) cc_final: 0.5078 (p0) REVERT: I 557 THR cc_start: 0.5796 (m) cc_final: 0.5015 (m) REVERT: J 172 LEU cc_start: 0.2824 (mt) cc_final: 0.2426 (tp) REVERT: J 301 ASN cc_start: 0.2691 (t0) cc_final: 0.2477 (t0) REVERT: J 326 ARG cc_start: 0.4740 (mtm-85) cc_final: 0.4242 (mtm110) REVERT: J 345 ASN cc_start: 0.6671 (p0) cc_final: 0.6292 (t0) REVERT: J 433 GLU cc_start: 0.6776 (pt0) cc_final: 0.6294 (mp0) REVERT: J 461 ILE cc_start: 0.2613 (OUTLIER) cc_final: 0.2327 (pt) REVERT: J 478 GLU cc_start: 0.7447 (tp30) cc_final: 0.6702 (pp20) REVERT: J 536 GLU cc_start: 0.6208 (tm-30) cc_final: 0.5925 (mp0) REVERT: J 550 LEU cc_start: 0.6920 (mt) cc_final: 0.6682 (tp) REVERT: J 554 PHE cc_start: 0.6824 (m-80) cc_final: 0.6560 (m-80) REVERT: J 557 THR cc_start: 0.5637 (m) cc_final: 0.5082 (m) REVERT: J 579 ASN cc_start: 0.7043 (m-40) cc_final: 0.6556 (p0) REVERT: K 259 GLU cc_start: 0.6350 (mm-30) cc_final: 0.5953 (mt-10) REVERT: K 312 MET cc_start: 0.7747 (tpp) cc_final: 0.7461 (mmm) REVERT: K 316 GLU cc_start: 0.7838 (tt0) cc_final: 0.7383 (tm-30) REVERT: K 365 PRO cc_start: 0.7258 (Cg_endo) cc_final: 0.6760 (Cg_exo) REVERT: K 433 GLU cc_start: 0.6565 (pt0) cc_final: 0.6188 (mp0) REVERT: K 478 GLU cc_start: 0.7493 (tp30) cc_final: 0.7019 (pp20) REVERT: K 534 THR cc_start: 0.7346 (m) cc_final: 0.6813 (m) REVERT: K 536 GLU cc_start: 0.6579 (tm-30) cc_final: 0.6156 (mp0) REVERT: K 550 LEU cc_start: 0.6906 (mt) cc_final: 0.6636 (tp) REVERT: K 567 MET cc_start: 0.5134 (mmm) cc_final: 0.4903 (mmm) REVERT: L 207 VAL cc_start: 0.2792 (OUTLIER) cc_final: 0.2493 (t) REVERT: L 345 ASN cc_start: 0.6665 (p0) cc_final: 0.6306 (t0) REVERT: L 407 MET cc_start: 0.2839 (tmm) cc_final: 0.2585 (tmm) REVERT: L 413 SER cc_start: 0.5413 (m) cc_final: 0.4798 (t) REVERT: L 429 MET cc_start: 0.5157 (mmm) cc_final: 0.4819 (mmm) REVERT: L 433 GLU cc_start: 0.6823 (pt0) cc_final: 0.6395 (mp0) REVERT: L 463 ARG cc_start: 0.2946 (OUTLIER) cc_final: 0.2571 (mtp85) REVERT: L 478 GLU cc_start: 0.7724 (tp30) cc_final: 0.7200 (pp20) REVERT: L 534 THR cc_start: 0.7344 (m) cc_final: 0.6674 (m) REVERT: L 536 GLU cc_start: 0.6421 (tm-30) cc_final: 0.5810 (mp0) REVERT: L 579 ASN cc_start: 0.6917 (m-40) cc_final: 0.6561 (p0) REVERT: M 345 ASN cc_start: 0.6533 (p0) cc_final: 0.6249 (t0) REVERT: M 429 MET cc_start: 0.4975 (mmm) cc_final: 0.4620 (mmm) REVERT: M 433 GLU cc_start: 0.6472 (pt0) cc_final: 0.5977 (mp0) REVERT: M 478 GLU cc_start: 0.7527 (tp30) cc_final: 0.6966 (pp20) REVERT: M 550 LEU cc_start: 0.6991 (mt) cc_final: 0.6696 (tp) REVERT: M 579 ASN cc_start: 0.6974 (m-40) cc_final: 0.6573 (p0) REVERT: N 174 TYR cc_start: 0.3228 (m-80) cc_final: 0.2689 (m-80) REVERT: N 298 GLU cc_start: 0.6345 (mm-30) cc_final: 0.5940 (mt-10) REVERT: N 312 MET cc_start: 0.7455 (tpp) cc_final: 0.7226 (mmm) REVERT: N 342 ASP cc_start: 0.6605 (OUTLIER) cc_final: 0.6376 (p0) REVERT: N 345 ASN cc_start: 0.6168 (p0) cc_final: 0.5673 (t0) REVERT: N 350 TRP cc_start: 0.4740 (m-10) cc_final: 0.4386 (m-90) REVERT: N 365 PRO cc_start: 0.7351 (Cg_endo) cc_final: 0.6955 (Cg_exo) REVERT: N 407 MET cc_start: 0.4198 (ttp) cc_final: 0.3020 (tmm) REVERT: N 413 SER cc_start: 0.4990 (m) cc_final: 0.4555 (t) REVERT: N 478 GLU cc_start: 0.7434 (tp30) cc_final: 0.6979 (pp20) REVERT: N 579 ASN cc_start: 0.6881 (m-40) cc_final: 0.6558 (p0) REVERT: O 172 LEU cc_start: 0.2930 (OUTLIER) cc_final: 0.2586 (mt) REVERT: O 207 VAL cc_start: 0.0883 (OUTLIER) cc_final: 0.0537 (t) REVERT: O 259 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5864 (mt-10) REVERT: O 301 ASN cc_start: 0.4327 (t0) cc_final: 0.4075 (m-40) REVERT: O 312 MET cc_start: 0.7790 (tpp) cc_final: 0.7574 (mmm) REVERT: O 365 PRO cc_start: 0.7126 (Cg_endo) cc_final: 0.6719 (Cg_exo) REVERT: O 407 MET cc_start: 0.3891 (OUTLIER) cc_final: 0.3337 (tmm) REVERT: O 433 GLU cc_start: 0.6305 (pt0) cc_final: 0.5981 (mt-10) REVERT: O 478 GLU cc_start: 0.7392 (tp30) cc_final: 0.6923 (pp20) REVERT: O 536 GLU cc_start: 0.6676 (tm-30) cc_final: 0.5974 (mp0) REVERT: O 550 LEU cc_start: 0.6985 (mt) cc_final: 0.6707 (tt) REVERT: O 553 LEU cc_start: 0.7562 (mt) cc_final: 0.7078 (tp) REVERT: O 579 ASN cc_start: 0.7192 (m-40) cc_final: 0.6817 (p0) outliers start: 275 outliers final: 85 residues processed: 1204 average time/residue: 0.5143 time to fit residues: 1057.3327 Evaluate side-chains 832 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 733 time to evaluate : 4.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 342 ASP Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 258 VAL Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain F residue 258 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 461 ILE Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 258 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 461 ILE Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 480 ASP Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 298 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 461 ILE Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 530 MET Chi-restraints excluded: chain L residue 172 LEU Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 394 ASN Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 463 ARG Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 190 ASP Chi-restraints excluded: chain M residue 423 THR Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 503 LEU Chi-restraints excluded: chain M residue 509 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain N residue 190 ASP Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 342 ASP Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 530 MET Chi-restraints excluded: chain O residue 172 LEU Chi-restraints excluded: chain O residue 190 ASP Chi-restraints excluded: chain O residue 207 VAL Chi-restraints excluded: chain O residue 258 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 407 MET Chi-restraints excluded: chain O residue 460 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 363 optimal weight: 30.0000 chunk 202 optimal weight: 5.9990 chunk 544 optimal weight: 7.9990 chunk 445 optimal weight: 3.9990 chunk 180 optimal weight: 0.8980 chunk 655 optimal weight: 4.9990 chunk 707 optimal weight: 5.9990 chunk 583 optimal weight: 2.9990 chunk 649 optimal weight: 20.0000 chunk 223 optimal weight: 3.9990 chunk 525 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 328 GLN B 440 GLN ** B 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 328 GLN C 404 ASN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 496 GLN C 533 GLN C 595 GLN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 188 ASN E 233 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN E 496 GLN ** E 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 328 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 ASN H 194 GLN H 328 GLN ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 ASN I 496 GLN ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 496 GLN ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 GLN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 496 GLN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 186 ASN ** O 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 496 GLN O 533 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3276 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 55485 Z= 0.329 Angle : 0.780 10.060 75255 Z= 0.400 Chirality : 0.049 0.205 9120 Planarity : 0.006 0.102 9855 Dihedral : 6.701 58.582 7826 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.58 % Favored : 95.00 % Rotamer: Outliers : 4.91 % Allowed : 18.94 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % 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: -2.07 (0.09), residues: 7200 helix: -0.36 (0.11), residues: 1950 sheet: -1.35 (0.09), residues: 2820 loop : -1.98 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 350 HIS 0.003 0.001 HIS A 133 PHE 0.019 0.003 PHE J 507 TYR 0.025 0.003 TYR H 134 ARG 0.007 0.001 ARG I 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 825 time to evaluate : 4.414 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 227 ILE cc_start: 0.7091 (mm) cc_final: 0.6632 (tp) REVERT: A 365 PRO cc_start: 0.7603 (Cg_endo) cc_final: 0.7257 (Cg_exo) REVERT: A 433 GLU cc_start: 0.6327 (pt0) cc_final: 0.6085 (pp20) REVERT: A 478 GLU cc_start: 0.7197 (tp30) cc_final: 0.6606 (pp20) REVERT: B 211 ARG cc_start: 0.5866 (mtt180) cc_final: 0.5424 (ptm160) REVERT: B 359 GLN cc_start: 0.5771 (tt0) cc_final: 0.5465 (tp40) REVERT: B 433 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5838 (mp0) REVERT: B 478 GLU cc_start: 0.7198 (tp30) cc_final: 0.6697 (pp20) REVERT: B 536 GLU cc_start: 0.5767 (tm-30) cc_final: 0.5277 (mp0) REVERT: B 550 LEU cc_start: 0.6935 (mt) cc_final: 0.6711 (tp) REVERT: B 602 GLN cc_start: 0.6734 (mt0) cc_final: 0.6495 (tp40) REVERT: C 211 ARG cc_start: 0.5698 (ttt180) cc_final: 0.5224 (ptt90) REVERT: C 238 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5411 (tp) REVERT: C 316 GLU cc_start: 0.7780 (tt0) cc_final: 0.7398 (tm-30) REVERT: C 365 PRO cc_start: 0.7538 (Cg_endo) cc_final: 0.7225 (Cg_exo) REVERT: C 433 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6605 (tt0) REVERT: C 550 LEU cc_start: 0.7307 (mt) cc_final: 0.7011 (tp) REVERT: D 312 MET cc_start: 0.7728 (tpp) cc_final: 0.7405 (mmm) REVERT: D 365 PRO cc_start: 0.7485 (Cg_endo) cc_final: 0.7218 (Cg_exo) REVERT: D 407 MET cc_start: 0.1513 (tmm) cc_final: 0.1289 (tmm) REVERT: D 433 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6532 (tt0) REVERT: D 550 LEU cc_start: 0.6664 (mt) cc_final: 0.6300 (tp) REVERT: D 554 PHE cc_start: 0.6833 (m-80) cc_final: 0.6630 (m-80) REVERT: E 174 TYR cc_start: 0.3243 (m-80) cc_final: 0.2954 (m-80) REVERT: E 179 GLU cc_start: 0.4890 (tm-30) cc_final: 0.4407 (tm-30) REVERT: E 336 VAL cc_start: 0.5761 (OUTLIER) cc_final: 0.5527 (m) REVERT: E 433 GLU cc_start: 0.5703 (pt0) cc_final: 0.5445 (mt-10) REVERT: E 478 GLU cc_start: 0.6968 (tp30) cc_final: 0.6589 (pp20) REVERT: E 522 GLU cc_start: 0.2337 (OUTLIER) cc_final: 0.1913 (tt0) REVERT: F 180 MET cc_start: 0.6974 (mmm) cc_final: 0.6583 (mmm) REVERT: F 312 MET cc_start: 0.6792 (tpp) cc_final: 0.6279 (mmm) REVERT: F 433 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6475 (tt0) REVERT: F 535 LYS cc_start: 0.7491 (ttmt) cc_final: 0.7238 (tttp) REVERT: G 433 GLU cc_start: 0.7139 (pt0) cc_final: 0.6816 (mt-10) REVERT: G 579 ASN cc_start: 0.7168 (t0) cc_final: 0.6789 (t0) REVERT: H 316 GLU cc_start: 0.8016 (tt0) cc_final: 0.7604 (tm-30) REVERT: H 365 PRO cc_start: 0.7620 (Cg_endo) cc_final: 0.7411 (Cg_exo) REVERT: H 407 MET cc_start: 0.5454 (ttp) cc_final: 0.4986 (tmm) REVERT: H 433 GLU cc_start: 0.6898 (pt0) cc_final: 0.6514 (mt-10) REVERT: I 228 ILE cc_start: 0.7194 (OUTLIER) cc_final: 0.6821 (pt) REVERT: I 407 MET cc_start: 0.3744 (ttt) cc_final: 0.3539 (ttt) REVERT: I 429 MET cc_start: 0.5372 (mmm) cc_final: 0.5117 (mmm) REVERT: I 433 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.6383 (tt0) REVERT: J 172 LEU cc_start: 0.3324 (mt) cc_final: 0.2937 (tp) REVERT: J 207 VAL cc_start: 0.3731 (OUTLIER) cc_final: 0.3041 (t) REVERT: J 326 ARG cc_start: 0.4876 (mtm-85) cc_final: 0.4391 (mtm110) REVERT: J 407 MET cc_start: 0.3203 (tmm) cc_final: 0.2920 (tmm) REVERT: J 433 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6613 (mt-10) REVERT: J 536 GLU cc_start: 0.6200 (tm-30) cc_final: 0.5778 (mp0) REVERT: J 550 LEU cc_start: 0.6904 (mt) cc_final: 0.6573 (tp) REVERT: J 554 PHE cc_start: 0.6938 (m-80) cc_final: 0.6721 (m-80) REVERT: J 598 ASP cc_start: 0.7568 (m-30) cc_final: 0.7342 (p0) REVERT: K 211 ARG cc_start: 0.6199 (mtt180) cc_final: 0.5743 (ptm-80) REVERT: K 312 MET cc_start: 0.7744 (tpp) cc_final: 0.7462 (mmm) REVERT: K 316 GLU cc_start: 0.7833 (tt0) cc_final: 0.7433 (tm-30) REVERT: K 365 PRO cc_start: 0.7547 (Cg_endo) cc_final: 0.7213 (Cg_exo) REVERT: K 433 GLU cc_start: 0.6667 (pt0) cc_final: 0.6342 (mp0) REVERT: K 490 VAL cc_start: 0.5518 (t) cc_final: 0.5313 (m) REVERT: K 550 LEU cc_start: 0.6895 (mt) cc_final: 0.6548 (tp) REVERT: K 567 MET cc_start: 0.5181 (mmm) cc_final: 0.4965 (mmm) REVERT: L 174 TYR cc_start: 0.3209 (m-80) cc_final: 0.2926 (m-80) REVERT: L 180 MET cc_start: 0.7020 (OUTLIER) cc_final: 0.6722 (mtt) REVERT: L 207 VAL cc_start: 0.3487 (OUTLIER) cc_final: 0.3002 (t) REVERT: L 211 ARG cc_start: 0.5544 (mtt180) cc_final: 0.5198 (ptm-80) REVERT: L 216 VAL cc_start: 0.6748 (t) cc_final: 0.6393 (t) REVERT: L 247 PHE cc_start: 0.4518 (m-80) cc_final: 0.4071 (m-80) REVERT: L 251 TYR cc_start: 0.5818 (m-80) cc_final: 0.5235 (m-80) REVERT: L 301 ASN cc_start: 0.2280 (t0) cc_final: 0.2065 (t0) REVERT: L 326 ARG cc_start: 0.3642 (mtm110) cc_final: 0.3301 (mtp-110) REVERT: L 407 MET cc_start: 0.3037 (tmm) cc_final: 0.2717 (tmm) REVERT: L 433 GLU cc_start: 0.6830 (pt0) cc_final: 0.6470 (mp0) REVERT: L 478 GLU cc_start: 0.7581 (tp30) cc_final: 0.7064 (pp20) REVERT: L 529 LEU cc_start: 0.4526 (OUTLIER) cc_final: 0.4309 (tp) REVERT: L 550 LEU cc_start: 0.7087 (mt) cc_final: 0.6801 (tp) REVERT: M 326 ARG cc_start: 0.3149 (mtm110) cc_final: 0.2932 (mtm110) REVERT: M 359 GLN cc_start: 0.5895 (tt0) cc_final: 0.5501 (tp40) REVERT: M 407 MET cc_start: 0.1296 (tmm) cc_final: 0.0839 (tmm) REVERT: M 429 MET cc_start: 0.5539 (mmm) cc_final: 0.5314 (mmm) REVERT: M 433 GLU cc_start: 0.6504 (OUTLIER) cc_final: 0.6169 (mt-10) REVERT: M 478 GLU cc_start: 0.7494 (tp30) cc_final: 0.6976 (pp20) REVERT: M 550 LEU cc_start: 0.6895 (mt) cc_final: 0.6639 (tp) REVERT: M 579 ASN cc_start: 0.7213 (m-40) cc_final: 0.6774 (p0) REVERT: N 174 TYR cc_start: 0.2911 (m-80) cc_final: 0.2701 (m-80) REVERT: N 211 ARG cc_start: 0.6101 (mtt180) cc_final: 0.5295 (ptm-80) REVERT: N 259 GLU cc_start: 0.5895 (mm-30) cc_final: 0.5406 (mt-10) REVERT: N 298 GLU cc_start: 0.6389 (mm-30) cc_final: 0.6182 (mt-10) REVERT: N 312 MET cc_start: 0.7776 (tpp) cc_final: 0.7450 (mmm) REVERT: N 365 PRO cc_start: 0.7295 (Cg_endo) cc_final: 0.7058 (Cg_exo) REVERT: N 407 MET cc_start: 0.4591 (ttp) cc_final: 0.3967 (tmm) REVERT: N 433 GLU cc_start: 0.5499 (pp20) cc_final: 0.5105 (tt0) REVERT: N 478 GLU cc_start: 0.7179 (tp30) cc_final: 0.6700 (pp20) REVERT: O 172 LEU cc_start: 0.3701 (mt) cc_final: 0.3488 (mt) REVERT: O 174 TYR cc_start: 0.3651 (m-80) cc_final: 0.2988 (m-80) REVERT: O 259 GLU cc_start: 0.5920 (mm-30) cc_final: 0.5493 (mt-10) REVERT: O 312 MET cc_start: 0.7903 (tpp) cc_final: 0.7588 (mmm) REVERT: O 365 PRO cc_start: 0.7462 (Cg_endo) cc_final: 0.7038 (Cg_exo) REVERT: O 429 MET cc_start: 0.5372 (mmm) cc_final: 0.5107 (mmm) REVERT: O 433 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5966 (mt-10) REVERT: O 478 GLU cc_start: 0.7171 (tp30) cc_final: 0.6754 (pp20) REVERT: O 553 LEU cc_start: 0.7363 (mt) cc_final: 0.7147 (tp) REVERT: O 598 ASP cc_start: 0.7457 (m-30) cc_final: 0.7093 (p0) outliers start: 297 outliers final: 177 residues processed: 1029 average time/residue: 0.5300 time to fit residues: 932.1166 Evaluate side-chains 867 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 674 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 430 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 337 GLU Chi-restraints excluded: chain C residue 350 TRP Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 430 ASP Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 185 THR Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 579 ASN Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 524 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 298 GLU Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 337 GLU Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 465 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 352 ASN Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 482 VAL Chi-restraints excluded: chain I residue 501 ASP Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 207 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 350 TRP Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 530 MET Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain K residue 141 LEU Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 258 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 336 VAL Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 530 MET Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 207 VAL Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 337 GLU Chi-restraints excluded: chain L residue 350 TRP Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 557 THR Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 258 VAL Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 350 TRP Chi-restraints excluded: chain M residue 423 THR Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain M residue 557 THR Chi-restraints excluded: chain M residue 587 ASN Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 342 ASP Chi-restraints excluded: chain N residue 416 THR Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 423 THR Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 557 THR Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 647 optimal weight: 6.9990 chunk 492 optimal weight: 30.0000 chunk 339 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 312 optimal weight: 1.9990 chunk 439 optimal weight: 3.9990 chunk 657 optimal weight: 0.9990 chunk 695 optimal weight: 0.0770 chunk 343 optimal weight: 9.9990 chunk 623 optimal weight: 30.0000 chunk 187 optimal weight: 0.9980 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 559 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 602 GLN ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 ASN G 138 ASN ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 HIS ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 GLN ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 233 GLN ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 GLN M 595 GLN ** N 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 328 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 233 GLN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3272 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55485 Z= 0.209 Angle : 0.684 12.782 75255 Z= 0.344 Chirality : 0.046 0.214 9120 Planarity : 0.005 0.089 9855 Dihedral : 5.845 58.411 7789 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.61 % Favored : 95.97 % Rotamer: Outliers : 4.05 % Allowed : 20.98 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.09), residues: 7200 helix: 0.11 (0.11), residues: 1950 sheet: -1.07 (0.09), residues: 2625 loop : -1.90 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 405 HIS 0.003 0.001 HIS A 133 PHE 0.014 0.002 PHE O 507 TYR 0.023 0.002 TYR H 134 ARG 0.006 0.000 ARG I 593 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 789 time to evaluate : 4.474 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 365 PRO cc_start: 0.7583 (Cg_endo) cc_final: 0.7243 (Cg_exo) REVERT: A 407 MET cc_start: 0.3357 (ttp) cc_final: 0.3084 (tmm) REVERT: A 478 GLU cc_start: 0.7252 (tp30) cc_final: 0.6659 (pp20) REVERT: B 172 LEU cc_start: 0.3307 (tp) cc_final: 0.2759 (tp) REVERT: B 211 ARG cc_start: 0.5954 (mtt180) cc_final: 0.5514 (ptm-80) REVERT: B 345 ASN cc_start: 0.6458 (OUTLIER) cc_final: 0.5899 (t0) REVERT: B 359 GLN cc_start: 0.5809 (tt0) cc_final: 0.5409 (tp40) REVERT: B 407 MET cc_start: 0.1951 (OUTLIER) cc_final: 0.1619 (tmm) REVERT: B 413 SER cc_start: 0.5525 (m) cc_final: 0.4820 (t) REVERT: B 433 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6312 (mt-10) REVERT: B 478 GLU cc_start: 0.7250 (tp30) cc_final: 0.6721 (pp20) REVERT: B 536 GLU cc_start: 0.5819 (tm-30) cc_final: 0.5533 (mp0) REVERT: B 550 LEU cc_start: 0.7063 (mt) cc_final: 0.6794 (tp) REVERT: B 602 GLN cc_start: 0.6791 (mt0) cc_final: 0.6560 (tp40) REVERT: C 211 ARG cc_start: 0.5737 (ttt180) cc_final: 0.5138 (ptm160) REVERT: C 238 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5170 (tp) REVERT: C 300 THR cc_start: 0.6858 (OUTLIER) cc_final: 0.6591 (p) REVERT: C 365 PRO cc_start: 0.7468 (Cg_endo) cc_final: 0.7151 (Cg_exo) REVERT: C 407 MET cc_start: 0.2479 (tmm) cc_final: 0.2105 (tmm) REVERT: C 433 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6569 (tt0) REVERT: C 550 LEU cc_start: 0.7346 (mt) cc_final: 0.7040 (tp) REVERT: C 579 ASN cc_start: 0.7530 (t0) cc_final: 0.7141 (t0) REVERT: D 179 GLU cc_start: 0.5458 (tm-30) cc_final: 0.5001 (tm-30) REVERT: D 238 LEU cc_start: 0.4782 (OUTLIER) cc_final: 0.4326 (tp) REVERT: D 297 ASP cc_start: 0.3834 (t70) cc_final: 0.3533 (t70) REVERT: D 312 MET cc_start: 0.7604 (tpp) cc_final: 0.7246 (mmm) REVERT: D 345 ASN cc_start: 0.6696 (OUTLIER) cc_final: 0.6251 (t0) REVERT: D 365 PRO cc_start: 0.7405 (Cg_endo) cc_final: 0.7065 (Cg_exo) REVERT: D 407 MET cc_start: 0.1931 (tmm) cc_final: 0.1545 (tmm) REVERT: D 433 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6394 (tt0) REVERT: D 475 GLN cc_start: 0.4371 (tt0) cc_final: 0.4125 (tm-30) REVERT: E 160 ASP cc_start: 0.4531 (t70) cc_final: 0.4258 (m-30) REVERT: E 365 PRO cc_start: 0.7671 (Cg_endo) cc_final: 0.7412 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5990 (pt0) cc_final: 0.5685 (mt-10) REVERT: E 478 GLU cc_start: 0.6948 (tp30) cc_final: 0.6543 (pp20) REVERT: F 100 MET cc_start: 0.2908 (mmt) cc_final: 0.2535 (mmm) REVERT: F 160 ASP cc_start: 0.6273 (t70) cc_final: 0.5895 (m-30) REVERT: F 230 MET cc_start: 0.6867 (mmt) cc_final: 0.6259 (tmm) REVERT: F 312 MET cc_start: 0.7092 (tpp) cc_final: 0.6622 (mmm) REVERT: F 358 THR cc_start: 0.3709 (OUTLIER) cc_final: 0.3299 (p) REVERT: F 433 GLU cc_start: 0.6797 (pt0) cc_final: 0.6438 (tt0) REVERT: F 535 LYS cc_start: 0.7432 (ttmt) cc_final: 0.7180 (tttp) REVERT: G 300 THR cc_start: 0.6001 (OUTLIER) cc_final: 0.5791 (p) REVERT: G 433 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: G 579 ASN cc_start: 0.7326 (t0) cc_final: 0.6980 (t0) REVERT: H 211 ARG cc_start: 0.5802 (mtt180) cc_final: 0.4941 (ppt170) REVERT: H 316 GLU cc_start: 0.8006 (tt0) cc_final: 0.7602 (tm-30) REVERT: H 407 MET cc_start: 0.5398 (ttp) cc_final: 0.5028 (tmm) REVERT: H 433 GLU cc_start: 0.6867 (pt0) cc_final: 0.6477 (mt-10) REVERT: I 407 MET cc_start: 0.3762 (ttt) cc_final: 0.3414 (tpp) REVERT: I 433 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6324 (tt0) REVERT: J 238 LEU cc_start: 0.5386 (OUTLIER) cc_final: 0.5073 (tp) REVERT: J 300 THR cc_start: 0.6771 (OUTLIER) cc_final: 0.6472 (p) REVERT: J 345 ASN cc_start: 0.6619 (OUTLIER) cc_final: 0.6269 (t0) REVERT: J 407 MET cc_start: 0.2921 (tmm) cc_final: 0.2520 (tmm) REVERT: J 429 MET cc_start: 0.5493 (mmm) cc_final: 0.5084 (mmm) REVERT: J 433 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6573 (mt-10) REVERT: J 478 GLU cc_start: 0.7369 (tp30) cc_final: 0.6717 (pp20) REVERT: J 536 GLU cc_start: 0.6171 (tm-30) cc_final: 0.5832 (mp0) REVERT: K 207 VAL cc_start: 0.1657 (OUTLIER) cc_final: 0.0574 (t) REVERT: K 211 ARG cc_start: 0.6296 (mtt180) cc_final: 0.6057 (ptm160) REVERT: K 300 THR cc_start: 0.6576 (OUTLIER) cc_final: 0.6292 (p) REVERT: K 312 MET cc_start: 0.7531 (tpp) cc_final: 0.7185 (mmm) REVERT: K 316 GLU cc_start: 0.7853 (tt0) cc_final: 0.7433 (tm-30) REVERT: K 433 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: L 174 TYR cc_start: 0.3088 (m-80) cc_final: 0.2492 (m-80) REVERT: L 211 ARG cc_start: 0.5608 (mtt180) cc_final: 0.5257 (ptm160) REVERT: L 251 TYR cc_start: 0.5657 (m-80) cc_final: 0.5109 (m-80) REVERT: L 407 MET cc_start: 0.3038 (tmm) cc_final: 0.2725 (tmm) REVERT: L 433 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: L 478 GLU cc_start: 0.7622 (tp30) cc_final: 0.7088 (pp20) REVERT: L 550 LEU cc_start: 0.6845 (mt) cc_final: 0.6610 (tp) REVERT: M 345 ASN cc_start: 0.6295 (OUTLIER) cc_final: 0.5833 (t0) REVERT: M 359 GLN cc_start: 0.5781 (tt0) cc_final: 0.5364 (tp40) REVERT: M 407 MET cc_start: 0.1610 (tmm) cc_final: 0.1190 (tmm) REVERT: M 433 GLU cc_start: 0.6492 (pt0) cc_final: 0.6157 (mt-10) REVERT: M 478 GLU cc_start: 0.7462 (tp30) cc_final: 0.6938 (pp20) REVERT: M 550 LEU cc_start: 0.6886 (mt) cc_final: 0.6626 (tp) REVERT: N 211 ARG cc_start: 0.5399 (mtt180) cc_final: 0.4959 (ptm-80) REVERT: N 238 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.4497 (tp) REVERT: N 259 GLU cc_start: 0.6084 (mm-30) cc_final: 0.5604 (mt-10) REVERT: N 298 GLU cc_start: 0.6487 (mm-30) cc_final: 0.6214 (mt-10) REVERT: N 345 ASN cc_start: 0.6442 (OUTLIER) cc_final: 0.5881 (t0) REVERT: N 433 GLU cc_start: 0.5471 (pp20) cc_final: 0.5058 (tt0) REVERT: N 478 GLU cc_start: 0.7188 (tp30) cc_final: 0.6695 (pp20) REVERT: N 574 ILE cc_start: 0.3759 (mt) cc_final: 0.3543 (mt) REVERT: O 179 GLU cc_start: 0.4884 (tm-30) cc_final: 0.4645 (tm-30) REVERT: O 259 GLU cc_start: 0.5979 (mm-30) cc_final: 0.5532 (mt-10) REVERT: O 312 MET cc_start: 0.7753 (tpp) cc_final: 0.7350 (mmm) REVERT: O 365 PRO cc_start: 0.7428 (Cg_endo) cc_final: 0.7212 (Cg_exo) REVERT: O 407 MET cc_start: 0.2981 (tmm) cc_final: 0.2421 (tmm) REVERT: O 433 GLU cc_start: 0.6276 (pt0) cc_final: 0.5931 (mt-10) REVERT: O 478 GLU cc_start: 0.7253 (tp30) cc_final: 0.6796 (pp20) REVERT: O 579 ASN cc_start: 0.7056 (t0) cc_final: 0.6760 (t0) outliers start: 245 outliers final: 144 residues processed: 968 average time/residue: 0.4795 time to fit residues: 807.9097 Evaluate side-chains 845 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 677 time to evaluate : 4.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 465 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 217 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 579 ASN Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 298 GLU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 482 VAL Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 352 ASN Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 482 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 345 ASN Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 207 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 433 GLU Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 308 GLN Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 541 VAL Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 345 ASN Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain M residue 587 ASN Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 423 THR Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 464 LYS Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 579 optimal weight: 3.9990 chunk 395 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 518 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 593 optimal weight: 0.0980 chunk 481 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 355 optimal weight: 2.9990 chunk 624 optimal weight: 40.0000 chunk 175 optimal weight: 5.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 ASN K 233 GLN ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 392 ASN ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 392 ASN ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 533 GLN ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 188 ASN ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 GLN ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 188 ASN N 233 GLN ** N 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 533 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3279 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 55485 Z= 0.229 Angle : 0.676 12.418 75255 Z= 0.342 Chirality : 0.046 0.245 9120 Planarity : 0.005 0.087 9855 Dihedral : 5.676 58.675 7789 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.83 % Favored : 94.75 % Rotamer: Outliers : 4.62 % Allowed : 21.57 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.10), residues: 7200 helix: 0.36 (0.11), residues: 1950 sheet: -0.98 (0.09), residues: 2700 loop : -1.90 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 350 HIS 0.003 0.001 HIS I 133 PHE 0.027 0.002 PHE J 393 TYR 0.024 0.002 TYR L 134 ARG 0.010 0.000 ARG K 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 729 time to evaluate : 4.417 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: A 345 ASN cc_start: 0.6498 (OUTLIER) cc_final: 0.5936 (t0) REVERT: A 365 PRO cc_start: 0.7596 (Cg_endo) cc_final: 0.7305 (Cg_exo) REVERT: A 433 GLU cc_start: 0.5970 (pp20) cc_final: 0.5621 (mt-10) REVERT: A 478 GLU cc_start: 0.7136 (tp30) cc_final: 0.6581 (pp20) REVERT: B 180 MET cc_start: 0.6642 (mtt) cc_final: 0.6308 (mtt) REVERT: B 211 ARG cc_start: 0.6023 (mtt180) cc_final: 0.5196 (ptm-80) REVERT: B 216 VAL cc_start: 0.7094 (t) cc_final: 0.6866 (t) REVERT: B 345 ASN cc_start: 0.6344 (OUTLIER) cc_final: 0.5840 (t0) REVERT: B 359 GLN cc_start: 0.5789 (tt0) cc_final: 0.5345 (tp40) REVERT: B 407 MET cc_start: 0.1915 (OUTLIER) cc_final: 0.1441 (tmm) REVERT: B 413 SER cc_start: 0.5561 (m) cc_final: 0.4867 (t) REVERT: B 433 GLU cc_start: 0.6658 (pt0) cc_final: 0.6262 (mt-10) REVERT: B 478 GLU cc_start: 0.7258 (tp30) cc_final: 0.6720 (pp20) REVERT: B 550 LEU cc_start: 0.7065 (mt) cc_final: 0.6811 (tp) REVERT: B 593 ARG cc_start: 0.7197 (OUTLIER) cc_final: 0.6792 (ttm-80) REVERT: B 602 GLN cc_start: 0.6658 (mt0) cc_final: 0.6454 (tp40) REVERT: C 211 ARG cc_start: 0.5834 (ttt180) cc_final: 0.5249 (ptt90) REVERT: C 238 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.5311 (tp) REVERT: C 300 THR cc_start: 0.6578 (OUTLIER) cc_final: 0.6327 (p) REVERT: C 345 ASN cc_start: 0.6684 (OUTLIER) cc_final: 0.6164 (t0) REVERT: C 365 PRO cc_start: 0.7105 (Cg_endo) cc_final: 0.6796 (Cg_exo) REVERT: C 433 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6588 (tt0) REVERT: C 579 ASN cc_start: 0.7398 (t0) cc_final: 0.7038 (t0) REVERT: D 180 MET cc_start: 0.6993 (mtt) cc_final: 0.6750 (mtt) REVERT: D 238 LEU cc_start: 0.4774 (OUTLIER) cc_final: 0.4224 (tp) REVERT: D 312 MET cc_start: 0.7549 (tpp) cc_final: 0.7291 (mmm) REVERT: D 345 ASN cc_start: 0.6316 (OUTLIER) cc_final: 0.5877 (t0) REVERT: D 365 PRO cc_start: 0.7103 (Cg_endo) cc_final: 0.6783 (Cg_exo) REVERT: D 407 MET cc_start: 0.1756 (tmm) cc_final: 0.1399 (tmm) REVERT: D 433 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6457 (tt0) REVERT: E 160 ASP cc_start: 0.4605 (t70) cc_final: 0.4299 (m-30) REVERT: E 238 LEU cc_start: 0.5498 (tp) cc_final: 0.5279 (mt) REVERT: E 300 THR cc_start: 0.5802 (OUTLIER) cc_final: 0.5555 (t) REVERT: E 365 PRO cc_start: 0.7682 (Cg_endo) cc_final: 0.7427 (Cg_exo) REVERT: E 433 GLU cc_start: 0.6073 (OUTLIER) cc_final: 0.5740 (mt-10) REVERT: E 478 GLU cc_start: 0.6813 (tp30) cc_final: 0.6428 (pp20) REVERT: F 100 MET cc_start: 0.2895 (mmt) cc_final: 0.2509 (mmm) REVERT: F 230 MET cc_start: 0.6836 (mmt) cc_final: 0.6370 (tmm) REVERT: F 297 ASP cc_start: 0.3824 (t0) cc_final: 0.3406 (t0) REVERT: F 312 MET cc_start: 0.7014 (tpp) cc_final: 0.6503 (mmm) REVERT: F 433 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.6448 (tt0) REVERT: F 535 LYS cc_start: 0.7565 (ttmt) cc_final: 0.7345 (tttp) REVERT: F 579 ASN cc_start: 0.6928 (t0) cc_final: 0.6618 (t0) REVERT: G 207 VAL cc_start: 0.2727 (OUTLIER) cc_final: 0.1994 (t) REVERT: G 216 VAL cc_start: 0.6206 (t) cc_final: 0.5986 (t) REVERT: G 297 ASP cc_start: 0.3750 (t0) cc_final: 0.3457 (t0) REVERT: G 433 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6871 (mt-10) REVERT: G 579 ASN cc_start: 0.7417 (t0) cc_final: 0.7098 (t0) REVERT: H 100 MET cc_start: 0.1427 (ttt) cc_final: 0.0772 (mmm) REVERT: H 211 ARG cc_start: 0.6007 (mtt180) cc_final: 0.5297 (ppt170) REVERT: H 316 GLU cc_start: 0.7837 (tt0) cc_final: 0.7448 (tm-30) REVERT: H 345 ASN cc_start: 0.6417 (OUTLIER) cc_final: 0.6055 (t0) REVERT: H 376 ASP cc_start: 0.5722 (m-30) cc_final: 0.5443 (p0) REVERT: H 407 MET cc_start: 0.5465 (ttp) cc_final: 0.4964 (tmm) REVERT: H 433 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6246 (mt-10) REVERT: H 536 GLU cc_start: 0.6378 (tm-30) cc_final: 0.6165 (tm-30) REVERT: H 579 ASN cc_start: 0.6981 (t0) cc_final: 0.6544 (t0) REVERT: I 433 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6347 (tt0) REVERT: J 174 TYR cc_start: 0.3460 (m-80) cc_final: 0.2912 (m-80) REVERT: J 238 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5054 (tp) REVERT: J 407 MET cc_start: 0.2913 (tmm) cc_final: 0.2488 (tmm) REVERT: J 433 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6667 (mt-10) REVERT: J 536 GLU cc_start: 0.6297 (tm-30) cc_final: 0.6059 (mp0) REVERT: K 300 THR cc_start: 0.6447 (OUTLIER) cc_final: 0.6185 (p) REVERT: K 312 MET cc_start: 0.7525 (tpp) cc_final: 0.7242 (mmm) REVERT: K 316 GLU cc_start: 0.7954 (tt0) cc_final: 0.7505 (tm-30) REVERT: K 433 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6277 (mp0) REVERT: L 180 MET cc_start: 0.7471 (mtt) cc_final: 0.7200 (mtt) REVERT: L 211 ARG cc_start: 0.5697 (mtt180) cc_final: 0.5440 (ptm160) REVERT: L 251 TYR cc_start: 0.5419 (m-80) cc_final: 0.5113 (m-80) REVERT: L 345 ASN cc_start: 0.6564 (OUTLIER) cc_final: 0.6074 (t0) REVERT: L 407 MET cc_start: 0.3539 (tmm) cc_final: 0.3216 (tmm) REVERT: L 433 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6696 (mt-10) REVERT: L 478 GLU cc_start: 0.7415 (tp30) cc_final: 0.6900 (pp20) REVERT: L 550 LEU cc_start: 0.6781 (mt) cc_final: 0.6548 (tp) REVERT: M 407 MET cc_start: 0.1959 (OUTLIER) cc_final: 0.1533 (tmm) REVERT: M 433 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6150 (mt-10) REVERT: M 550 LEU cc_start: 0.6870 (mt) cc_final: 0.6609 (tp) REVERT: N 238 LEU cc_start: 0.4886 (OUTLIER) cc_final: 0.4613 (tp) REVERT: N 259 GLU cc_start: 0.6044 (mm-30) cc_final: 0.5523 (mt-10) REVERT: N 298 GLU cc_start: 0.6515 (mm-30) cc_final: 0.6275 (mt-10) REVERT: N 345 ASN cc_start: 0.6671 (OUTLIER) cc_final: 0.6073 (t0) REVERT: N 359 GLN cc_start: 0.6009 (tt0) cc_final: 0.5692 (tp40) REVERT: N 433 GLU cc_start: 0.5392 (pp20) cc_final: 0.5029 (mt-10) REVERT: N 478 GLU cc_start: 0.7185 (tp30) cc_final: 0.6701 (pp20) REVERT: N 579 ASN cc_start: 0.7465 (t0) cc_final: 0.7035 (t0) REVERT: N 593 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6895 (mtp85) REVERT: O 211 ARG cc_start: 0.5593 (ttt180) cc_final: 0.4744 (ptm160) REVERT: O 259 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5751 (mt-10) REVERT: O 312 MET cc_start: 0.7794 (tpp) cc_final: 0.7485 (mmm) REVERT: O 365 PRO cc_start: 0.7150 (Cg_endo) cc_final: 0.6806 (Cg_exo) REVERT: O 429 MET cc_start: 0.5297 (mmm) cc_final: 0.5041 (mmm) REVERT: O 433 GLU cc_start: 0.6269 (OUTLIER) cc_final: 0.5930 (mt-10) REVERT: O 550 LEU cc_start: 0.7112 (mt) cc_final: 0.6693 (tp) REVERT: O 579 ASN cc_start: 0.7042 (t0) cc_final: 0.6745 (t0) outliers start: 279 outliers final: 182 residues processed: 929 average time/residue: 0.4840 time to fit residues: 780.4278 Evaluate side-chains 863 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 650 time to evaluate : 4.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 300 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 258 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 300 THR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 522 GLU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 298 GLU Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 475 GLN Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 541 VAL Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 352 ASN Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 300 THR Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 336 VAL Chi-restraints excluded: chain K residue 416 THR Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 433 GLU Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 345 ASN Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 613 VAL Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 217 VAL Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 423 THR Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 530 MET Chi-restraints excluded: chain M residue 541 VAL Chi-restraints excluded: chain M residue 587 ASN Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 342 ASP Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain N residue 593 ARG Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 423 THR Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 234 optimal weight: 5.9990 chunk 626 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 chunk 408 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 696 optimal weight: 9.9990 chunk 578 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 57 optimal weight: 20.0000 chunk 230 optimal weight: 5.9990 chunk 365 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 GLN ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 186 ASN I 233 GLN ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 496 GLN O 533 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3282 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55485 Z= 0.232 Angle : 0.667 11.562 75255 Z= 0.339 Chirality : 0.046 0.199 9120 Planarity : 0.005 0.084 9855 Dihedral : 5.602 57.851 7789 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.89 % Favored : 94.69 % Rotamer: Outliers : 4.83 % Allowed : 22.10 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.10), residues: 7200 helix: 0.39 (0.11), residues: 2040 sheet: -0.85 (0.10), residues: 2640 loop : -2.06 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 405 HIS 0.003 0.001 HIS G 133 PHE 0.027 0.002 PHE H 393 TYR 0.032 0.002 TYR B 134 ARG 0.007 0.000 ARG N 245 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 686 time to evaluate : 4.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6566 (t0) REVERT: A 365 PRO cc_start: 0.7284 (Cg_endo) cc_final: 0.6927 (Cg_exo) REVERT: A 423 THR cc_start: 0.6135 (OUTLIER) cc_final: 0.5919 (p) REVERT: A 478 GLU cc_start: 0.7171 (tp30) cc_final: 0.6679 (pp20) REVERT: B 211 ARG cc_start: 0.5785 (mtt180) cc_final: 0.5549 (ptm-80) REVERT: B 345 ASN cc_start: 0.6411 (OUTLIER) cc_final: 0.5834 (t0) REVERT: B 359 GLN cc_start: 0.5883 (tt0) cc_final: 0.5501 (tp40) REVERT: B 413 SER cc_start: 0.5536 (m) cc_final: 0.4935 (t) REVERT: B 433 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6319 (mt-10) REVERT: B 478 GLU cc_start: 0.7271 (tp30) cc_final: 0.6724 (pp20) REVERT: B 550 LEU cc_start: 0.6976 (mt) cc_final: 0.6724 (tp) REVERT: B 593 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6847 (ttm-80) REVERT: C 211 ARG cc_start: 0.6027 (ttt180) cc_final: 0.5288 (ptt90) REVERT: C 238 LEU cc_start: 0.5824 (OUTLIER) cc_final: 0.5331 (tp) REVERT: C 345 ASN cc_start: 0.6636 (OUTLIER) cc_final: 0.6185 (t0) REVERT: C 365 PRO cc_start: 0.7196 (Cg_endo) cc_final: 0.6865 (Cg_exo) REVERT: C 433 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6576 (tt0) REVERT: C 579 ASN cc_start: 0.7429 (t0) cc_final: 0.7070 (t0) REVERT: D 207 VAL cc_start: 0.2509 (OUTLIER) cc_final: 0.1732 (t) REVERT: D 238 LEU cc_start: 0.4981 (OUTLIER) cc_final: 0.4466 (tt) REVERT: D 312 MET cc_start: 0.7545 (tpp) cc_final: 0.7034 (mmm) REVERT: D 365 PRO cc_start: 0.7138 (Cg_endo) cc_final: 0.6816 (Cg_exo) REVERT: D 407 MET cc_start: 0.2100 (tmm) cc_final: 0.1674 (tmm) REVERT: D 433 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5987 (mt-10) REVERT: E 160 ASP cc_start: 0.4501 (t70) cc_final: 0.4209 (m-30) REVERT: E 365 PRO cc_start: 0.7661 (Cg_endo) cc_final: 0.7398 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5832 (OUTLIER) cc_final: 0.5457 (mt-10) REVERT: E 478 GLU cc_start: 0.6848 (tp30) cc_final: 0.6451 (pp20) REVERT: F 100 MET cc_start: 0.2747 (mmt) cc_final: 0.2363 (mmm) REVERT: F 160 ASP cc_start: 0.6459 (t70) cc_final: 0.6040 (m-30) REVERT: F 207 VAL cc_start: 0.2980 (OUTLIER) cc_final: 0.2516 (t) REVERT: F 230 MET cc_start: 0.6832 (mmt) cc_final: 0.6359 (tmm) REVERT: F 312 MET cc_start: 0.7270 (tpp) cc_final: 0.6829 (mmm) REVERT: F 358 THR cc_start: 0.3767 (OUTLIER) cc_final: 0.3260 (p) REVERT: F 433 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: F 535 LYS cc_start: 0.7704 (ttmt) cc_final: 0.7494 (tttp) REVERT: F 579 ASN cc_start: 0.6992 (t0) cc_final: 0.6690 (t0) REVERT: G 160 ASP cc_start: 0.6231 (t70) cc_final: 0.5846 (t70) REVERT: G 407 MET cc_start: 0.3315 (tmm) cc_final: 0.3060 (tmm) REVERT: G 433 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6866 (mt-10) REVERT: G 579 ASN cc_start: 0.7346 (t0) cc_final: 0.7014 (t0) REVERT: H 100 MET cc_start: 0.1383 (ttt) cc_final: -0.0274 (mtp) REVERT: H 316 GLU cc_start: 0.7847 (tt0) cc_final: 0.7455 (tm-30) REVERT: H 345 ASN cc_start: 0.6453 (OUTLIER) cc_final: 0.6031 (t0) REVERT: H 376 ASP cc_start: 0.5691 (m-30) cc_final: 0.5425 (p0) REVERT: H 407 MET cc_start: 0.5559 (ttp) cc_final: 0.5100 (tmm) REVERT: H 433 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6049 (mt-10) REVERT: H 579 ASN cc_start: 0.6998 (t0) cc_final: 0.6547 (t0) REVERT: I 407 MET cc_start: 0.1859 (tmm) cc_final: 0.1602 (tmm) REVERT: I 433 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6373 (tt0) REVERT: I 478 GLU cc_start: 0.7478 (tp30) cc_final: 0.7169 (pp20) REVERT: J 238 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5404 (tp) REVERT: J 300 THR cc_start: 0.6768 (OUTLIER) cc_final: 0.6517 (p) REVERT: J 345 ASN cc_start: 0.6688 (OUTLIER) cc_final: 0.6458 (t0) REVERT: J 407 MET cc_start: 0.2565 (tmm) cc_final: 0.2319 (tmm) REVERT: J 433 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6448 (mt-10) REVERT: K 312 MET cc_start: 0.7420 (tpp) cc_final: 0.7045 (mmm) REVERT: K 316 GLU cc_start: 0.8032 (tt0) cc_final: 0.7591 (tm-30) REVERT: K 579 ASN cc_start: 0.7193 (t0) cc_final: 0.6892 (t0) REVERT: L 174 TYR cc_start: 0.3178 (m-80) cc_final: 0.2658 (m-80) REVERT: L 211 ARG cc_start: 0.5806 (mtt180) cc_final: 0.5536 (ptm160) REVERT: L 251 TYR cc_start: 0.5230 (m-80) cc_final: 0.4970 (m-80) REVERT: L 345 ASN cc_start: 0.6367 (OUTLIER) cc_final: 0.5842 (t0) REVERT: L 359 GLN cc_start: 0.5627 (tt0) cc_final: 0.5373 (tp-100) REVERT: L 407 MET cc_start: 0.3601 (tmm) cc_final: 0.3278 (tmm) REVERT: L 433 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: L 478 GLU cc_start: 0.7359 (tp30) cc_final: 0.6897 (pp20) REVERT: L 481 SER cc_start: 0.5560 (m) cc_final: 0.5234 (p) REVERT: L 550 LEU cc_start: 0.6973 (mt) cc_final: 0.6717 (tp) REVERT: M 345 ASN cc_start: 0.6432 (OUTLIER) cc_final: 0.5968 (t0) REVERT: M 407 MET cc_start: 0.2083 (OUTLIER) cc_final: 0.1640 (tmm) REVERT: M 433 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6116 (mt-10) REVERT: M 550 LEU cc_start: 0.6953 (mt) cc_final: 0.6724 (tp) REVERT: N 238 LEU cc_start: 0.4948 (OUTLIER) cc_final: 0.4506 (tp) REVERT: N 345 ASN cc_start: 0.6723 (OUTLIER) cc_final: 0.6061 (t0) REVERT: N 407 MET cc_start: 0.3022 (ttp) cc_final: 0.2763 (tmm) REVERT: N 413 SER cc_start: 0.5638 (m) cc_final: 0.5141 (t) REVERT: N 433 GLU cc_start: 0.5451 (pp20) cc_final: 0.5064 (mt-10) REVERT: N 478 GLU cc_start: 0.7191 (tp30) cc_final: 0.6695 (pp20) REVERT: N 579 ASN cc_start: 0.7560 (t0) cc_final: 0.7159 (t0) REVERT: O 211 ARG cc_start: 0.5690 (ttt180) cc_final: 0.4859 (ptm160) REVERT: O 259 GLU cc_start: 0.6280 (mm-30) cc_final: 0.5768 (mt-10) REVERT: O 312 MET cc_start: 0.7705 (tpp) cc_final: 0.7456 (mmm) REVERT: O 365 PRO cc_start: 0.7222 (Cg_endo) cc_final: 0.6859 (Cg_exo) REVERT: O 407 MET cc_start: 0.2261 (tmm) cc_final: 0.1989 (tmm) REVERT: O 429 MET cc_start: 0.5456 (mmm) cc_final: 0.5198 (mmm) REVERT: O 433 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.6007 (mt-10) REVERT: O 579 ASN cc_start: 0.7103 (t0) cc_final: 0.6831 (t0) outliers start: 292 outliers final: 188 residues processed: 894 average time/residue: 0.5165 time to fit residues: 806.9737 Evaluate side-chains 836 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 617 time to evaluate : 5.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 423 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 541 VAL Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain F residue 207 VAL Chi-restraints excluded: chain F residue 217 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 573 THR Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 475 GLN Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 574 ILE Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 345 ASN Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 167 VAL Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 423 THR Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 345 ASN Chi-restraints excluded: chain L residue 367 ILE Chi-restraints excluded: chain L residue 423 THR Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 445 GLN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 573 THR Chi-restraints excluded: chain L residue 613 VAL Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 345 ASN Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 423 THR Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 482 VAL Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 587 ASN Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 300 THR Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 336 VAL Chi-restraints excluded: chain N residue 342 ASP Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 423 THR Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 671 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 396 optimal weight: 9.9990 chunk 508 optimal weight: 0.0470 chunk 394 optimal weight: 50.0000 chunk 586 optimal weight: 20.0000 chunk 389 optimal weight: 20.0000 chunk 693 optimal weight: 8.9990 chunk 434 optimal weight: 20.0000 chunk 423 optimal weight: 8.9990 chunk 320 optimal weight: 1.9990 overall best weight: 4.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 213 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 213 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 440 GLN ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 496 GLN ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 440 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 496 GLN ** F 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 440 GLN ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 496 GLN G 533 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 602 GLN ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 440 GLN M 488 GLN M 496 GLN M 533 GLN ** M 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 587 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 496 GLN ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 602 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3288 moved from start: 0.6277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 55485 Z= 0.379 Angle : 0.782 13.353 75255 Z= 0.399 Chirality : 0.050 0.420 9120 Planarity : 0.006 0.088 9855 Dihedral : 6.031 59.188 7789 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.40 % Allowed : 7.11 % Favored : 92.49 % Rotamer: Outliers : 5.06 % Allowed : 22.73 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.10), residues: 7200 helix: 0.25 (0.11), residues: 2040 sheet: -1.17 (0.10), residues: 2640 loop : -2.36 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 350 HIS 0.005 0.001 HIS K 133 PHE 0.035 0.003 PHE J 592 TYR 0.026 0.003 TYR L 134 ARG 0.010 0.001 ARG H 158 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 645 time to evaluate : 4.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 ASN cc_start: 0.3605 (OUTLIER) cc_final: 0.3370 (t0) REVERT: A 345 ASN cc_start: 0.6852 (OUTLIER) cc_final: 0.6595 (t0) REVERT: A 365 PRO cc_start: 0.7160 (Cg_endo) cc_final: 0.6805 (Cg_exo) REVERT: B 211 ARG cc_start: 0.5262 (mtt180) cc_final: 0.4978 (ptm160) REVERT: B 345 ASN cc_start: 0.6445 (OUTLIER) cc_final: 0.6043 (t0) REVERT: B 407 MET cc_start: 0.4254 (OUTLIER) cc_final: 0.4013 (tmm) REVERT: B 413 SER cc_start: 0.5436 (m) cc_final: 0.4822 (t) REVERT: B 433 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6053 (mt-10) REVERT: B 593 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6798 (ttm-80) REVERT: C 211 ARG cc_start: 0.6008 (ttt180) cc_final: 0.5391 (ptm-80) REVERT: C 238 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5558 (tp) REVERT: C 345 ASN cc_start: 0.6301 (OUTLIER) cc_final: 0.5995 (t0) REVERT: C 365 PRO cc_start: 0.7335 (Cg_endo) cc_final: 0.7060 (Cg_exo) REVERT: C 433 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: C 579 ASN cc_start: 0.7468 (t0) cc_final: 0.7098 (t0) REVERT: C 593 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.7109 (ttt90) REVERT: D 180 MET cc_start: 0.6792 (mtt) cc_final: 0.6527 (mtm) REVERT: D 238 LEU cc_start: 0.4934 (OUTLIER) cc_final: 0.4411 (tp) REVERT: D 312 MET cc_start: 0.7363 (tpp) cc_final: 0.6886 (tpp) REVERT: D 345 ASN cc_start: 0.6276 (OUTLIER) cc_final: 0.5841 (t0) REVERT: D 365 PRO cc_start: 0.7262 (Cg_endo) cc_final: 0.6948 (Cg_exo) REVERT: D 376 ASP cc_start: 0.5951 (OUTLIER) cc_final: 0.5723 (p0) REVERT: D 407 MET cc_start: 0.2185 (tmm) cc_final: 0.1693 (tmm) REVERT: D 433 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5915 (mt-10) REVERT: E 160 ASP cc_start: 0.4366 (t70) cc_final: 0.4041 (m-30) REVERT: E 365 PRO cc_start: 0.7780 (Cg_endo) cc_final: 0.7539 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5830 (OUTLIER) cc_final: 0.5483 (mt-10) REVERT: E 478 GLU cc_start: 0.6862 (tp30) cc_final: 0.6462 (pp20) REVERT: F 100 MET cc_start: 0.2669 (mmt) cc_final: 0.2415 (mmm) REVERT: F 160 ASP cc_start: 0.6403 (t70) cc_final: 0.5998 (t0) REVERT: F 230 MET cc_start: 0.6419 (mmt) cc_final: 0.6074 (tmm) REVERT: F 358 THR cc_start: 0.4117 (OUTLIER) cc_final: 0.3653 (p) REVERT: F 433 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6305 (mt-10) REVERT: F 579 ASN cc_start: 0.7288 (t0) cc_final: 0.6988 (t0) REVERT: G 141 LEU cc_start: -0.0617 (OUTLIER) cc_final: -0.0925 (tp) REVERT: G 160 ASP cc_start: 0.6290 (t70) cc_final: 0.5793 (t70) REVERT: G 180 MET cc_start: 0.6938 (mmt) cc_final: 0.6473 (mmt) REVERT: G 433 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: G 579 ASN cc_start: 0.7241 (t0) cc_final: 0.6921 (t0) REVERT: H 316 GLU cc_start: 0.7946 (tt0) cc_final: 0.7505 (tm-30) REVERT: H 345 ASN cc_start: 0.6549 (OUTLIER) cc_final: 0.6259 (t0) REVERT: H 376 ASP cc_start: 0.5752 (m-30) cc_final: 0.5501 (p0) REVERT: H 433 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5806 (mt-10) REVERT: H 579 ASN cc_start: 0.7064 (t0) cc_final: 0.6655 (t0) REVERT: I 228 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.6891 (mm) REVERT: I 433 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6646 (tm-30) REVERT: J 238 LEU cc_start: 0.5759 (OUTLIER) cc_final: 0.5317 (tp) REVERT: J 345 ASN cc_start: 0.6451 (OUTLIER) cc_final: 0.6184 (t0) REVERT: J 433 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6655 (mt-10) REVERT: K 312 MET cc_start: 0.7274 (tpp) cc_final: 0.6899 (mmm) REVERT: K 316 GLU cc_start: 0.7913 (tt0) cc_final: 0.7518 (tm-30) REVERT: K 481 SER cc_start: 0.6034 (m) cc_final: 0.5650 (p) REVERT: L 211 ARG cc_start: 0.5826 (mtt180) cc_final: 0.5490 (ptm160) REVERT: L 251 TYR cc_start: 0.5213 (m-80) cc_final: 0.4952 (m-80) REVERT: L 345 ASN cc_start: 0.6164 (OUTLIER) cc_final: 0.5642 (t0) REVERT: L 433 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6715 (tm-30) REVERT: L 481 SER cc_start: 0.5645 (m) cc_final: 0.5312 (p) REVERT: L 550 LEU cc_start: 0.6920 (mt) cc_final: 0.6657 (tp) REVERT: M 345 ASN cc_start: 0.6182 (OUTLIER) cc_final: 0.5720 (t0) REVERT: M 407 MET cc_start: 0.2376 (OUTLIER) cc_final: 0.1908 (tmm) REVERT: M 433 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5806 (mt-10) REVERT: N 211 ARG cc_start: 0.5638 (ttt180) cc_final: 0.5076 (ptt90) REVERT: N 238 LEU cc_start: 0.5014 (OUTLIER) cc_final: 0.4558 (tp) REVERT: N 345 ASN cc_start: 0.6652 (OUTLIER) cc_final: 0.6125 (t0) REVERT: N 376 ASP cc_start: 0.5723 (m-30) cc_final: 0.5509 (p0) REVERT: N 413 SER cc_start: 0.5573 (m) cc_final: 0.4984 (t) REVERT: N 429 MET cc_start: 0.5964 (mmm) cc_final: 0.5728 (mmm) REVERT: N 433 GLU cc_start: 0.5628 (pp20) cc_final: 0.5202 (mt-10) REVERT: N 579 ASN cc_start: 0.7605 (t0) cc_final: 0.7212 (t0) REVERT: O 211 ARG cc_start: 0.6012 (ttt180) cc_final: 0.5070 (ptm-80) REVERT: O 312 MET cc_start: 0.7545 (tpp) cc_final: 0.7296 (mmm) REVERT: O 365 PRO cc_start: 0.7357 (Cg_endo) cc_final: 0.7025 (Cg_exo) REVERT: O 407 MET cc_start: 0.2304 (tmm) cc_final: 0.2096 (tmm) REVERT: O 429 MET cc_start: 0.5344 (mmm) cc_final: 0.5064 (mmm) REVERT: O 433 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6126 (mt-10) outliers start: 306 outliers final: 208 residues processed: 873 average time/residue: 0.4870 time to fit residues: 738.8043 Evaluate side-chains 830 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 588 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 407 MET Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 557 THR Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 376 ASP Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 337 GLU Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 503 LEU Chi-restraints excluded: chain F residue 509 THR Chi-restraints excluded: chain F residue 559 ASN Chi-restraints excluded: chain F residue 573 THR Chi-restraints excluded: chain G residue 141 LEU Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 251 TYR Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 475 GLN Chi-restraints excluded: chain H residue 509 THR Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 530 MET Chi-restraints excluded: chain H residue 593 ARG Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 228 ILE Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain I residue 386 LEU Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 503 LEU Chi-restraints excluded: chain I residue 529 LEU Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 345 ASN Chi-restraints excluded: chain J residue 423 THR Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 466 VAL Chi-restraints excluded: chain J residue 468 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 503 LEU Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 541 VAL Chi-restraints excluded: chain J residue 593 ARG Chi-restraints excluded: chain K residue 181 VAL Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 541 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 185 THR Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 345 ASN Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 503 LEU Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 573 THR Chi-restraints excluded: chain L residue 613 VAL Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 209 ASP Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 345 ASN Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 423 THR Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 524 VAL Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 587 ASN Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 337 GLU Chi-restraints excluded: chain N residue 342 ASP Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 423 THR Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 185 THR Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 337 GLU Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 423 THR Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 503 LEU Chi-restraints excluded: chain O residue 512 VAL Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 541 VAL Chi-restraints excluded: chain O residue 553 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 429 optimal weight: 10.0000 chunk 277 optimal weight: 0.8980 chunk 414 optimal weight: 0.7980 chunk 209 optimal weight: 8.9990 chunk 136 optimal weight: 5.9990 chunk 134 optimal weight: 0.8980 chunk 441 optimal weight: 20.0000 chunk 472 optimal weight: 20.0000 chunk 343 optimal weight: 0.0980 chunk 64 optimal weight: 0.9990 chunk 545 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 301 ASN ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 233 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN ** H 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 GLN ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 587 ASN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3286 moved from start: 0.6412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55485 Z= 0.186 Angle : 0.679 13.752 75255 Z= 0.337 Chirality : 0.047 0.391 9120 Planarity : 0.005 0.066 9855 Dihedral : 5.665 47.961 7787 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.85 % Favored : 95.89 % Rotamer: Outliers : 3.66 % Allowed : 24.48 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.10), residues: 7200 helix: 0.48 (0.11), residues: 2040 sheet: -0.91 (0.10), residues: 2640 loop : -2.17 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 405 HIS 0.003 0.001 HIS G 133 PHE 0.032 0.002 PHE J 592 TYR 0.023 0.002 TYR G 134 ARG 0.009 0.000 ARG I 224 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 659 time to evaluate : 4.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.6856 (OUTLIER) cc_final: 0.6631 (t0) REVERT: A 365 PRO cc_start: 0.7090 (Cg_endo) cc_final: 0.6704 (Cg_exo) REVERT: A 433 GLU cc_start: 0.6060 (mt-10) cc_final: 0.5756 (tm-30) REVERT: B 345 ASN cc_start: 0.6265 (OUTLIER) cc_final: 0.5723 (t0) REVERT: B 413 SER cc_start: 0.5455 (m) cc_final: 0.4913 (t) REVERT: B 433 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6375 (mt-10) REVERT: C 211 ARG cc_start: 0.6347 (ttt180) cc_final: 0.5735 (ptm-80) REVERT: C 238 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5067 (tp) REVERT: C 345 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.6165 (t0) REVERT: C 365 PRO cc_start: 0.7334 (Cg_endo) cc_final: 0.7010 (Cg_exo) REVERT: C 413 SER cc_start: 0.5578 (m) cc_final: 0.4929 (t) REVERT: C 433 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6569 (mt-10) REVERT: C 579 ASN cc_start: 0.7507 (t0) cc_final: 0.7190 (t0) REVERT: D 182 ARG cc_start: 0.6425 (ttm110) cc_final: 0.6206 (mtm-85) REVERT: D 238 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4522 (tt) REVERT: D 312 MET cc_start: 0.7364 (tpp) cc_final: 0.6934 (tpp) REVERT: D 345 ASN cc_start: 0.6311 (OUTLIER) cc_final: 0.5850 (t0) REVERT: D 365 PRO cc_start: 0.7108 (Cg_endo) cc_final: 0.6762 (Cg_exo) REVERT: D 376 ASP cc_start: 0.5916 (m-30) cc_final: 0.5706 (p0) REVERT: D 407 MET cc_start: 0.2555 (tmm) cc_final: 0.2050 (tmm) REVERT: D 413 SER cc_start: 0.4862 (m) cc_final: 0.4288 (t) REVERT: D 433 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5922 (mt-10) REVERT: D 579 ASN cc_start: 0.7634 (t0) cc_final: 0.7342 (t0) REVERT: E 160 ASP cc_start: 0.4547 (t70) cc_final: 0.4258 (m-30) REVERT: E 365 PRO cc_start: 0.7656 (Cg_endo) cc_final: 0.7405 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5812 (OUTLIER) cc_final: 0.5439 (mt-10) REVERT: E 478 GLU cc_start: 0.6859 (tp30) cc_final: 0.6456 (pp20) REVERT: F 100 MET cc_start: 0.2721 (mmt) cc_final: 0.2461 (mmm) REVERT: F 160 ASP cc_start: 0.6415 (t70) cc_final: 0.6022 (t0) REVERT: F 230 MET cc_start: 0.6658 (mmt) cc_final: 0.6278 (tmm) REVERT: F 312 MET cc_start: 0.7772 (tpt) cc_final: 0.7239 (mmm) REVERT: F 358 THR cc_start: 0.3841 (OUTLIER) cc_final: 0.3360 (p) REVERT: F 433 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6037 (mt-10) REVERT: F 579 ASN cc_start: 0.7295 (t0) cc_final: 0.6923 (t0) REVERT: G 160 ASP cc_start: 0.6334 (t70) cc_final: 0.5859 (t70) REVERT: G 407 MET cc_start: 0.3302 (tmm) cc_final: 0.3063 (tmm) REVERT: G 433 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: G 579 ASN cc_start: 0.7307 (t0) cc_final: 0.6975 (t0) REVERT: H 100 MET cc_start: 0.1333 (ttt) cc_final: -0.0233 (mtp) REVERT: H 211 ARG cc_start: 0.5818 (mtt180) cc_final: 0.5589 (ptt90) REVERT: H 316 GLU cc_start: 0.7812 (tt0) cc_final: 0.7403 (tm-30) REVERT: H 345 ASN cc_start: 0.6470 (OUTLIER) cc_final: 0.6126 (t0) REVERT: H 376 ASP cc_start: 0.5699 (m-30) cc_final: 0.5492 (p0) REVERT: H 433 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.5984 (mt-10) REVERT: H 579 ASN cc_start: 0.7090 (t0) cc_final: 0.6684 (t0) REVERT: I 433 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6714 (tm-30) REVERT: I 478 GLU cc_start: 0.7609 (tp30) cc_final: 0.7264 (pp20) REVERT: J 238 LEU cc_start: 0.5692 (OUTLIER) cc_final: 0.5317 (tp) REVERT: J 345 ASN cc_start: 0.6695 (OUTLIER) cc_final: 0.6452 (t0) REVERT: J 433 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6581 (mt-10) REVERT: K 312 MET cc_start: 0.7326 (tpp) cc_final: 0.6867 (tpp) REVERT: K 316 GLU cc_start: 0.7904 (tt0) cc_final: 0.7497 (tm-30) REVERT: K 579 ASN cc_start: 0.7204 (t0) cc_final: 0.6888 (t0) REVERT: L 211 ARG cc_start: 0.5765 (mtt180) cc_final: 0.5423 (ptm-80) REVERT: L 251 TYR cc_start: 0.5230 (m-80) cc_final: 0.5024 (m-80) REVERT: L 345 ASN cc_start: 0.6458 (OUTLIER) cc_final: 0.5908 (t0) REVERT: L 407 MET cc_start: 0.3253 (tmm) cc_final: 0.3026 (tmm) REVERT: L 433 GLU cc_start: 0.6891 (pt0) cc_final: 0.6573 (mt-10) REVERT: L 481 SER cc_start: 0.5897 (m) cc_final: 0.5590 (p) REVERT: L 550 LEU cc_start: 0.7027 (mt) cc_final: 0.6769 (tp) REVERT: M 174 TYR cc_start: 0.3605 (m-80) cc_final: 0.3399 (m-10) REVERT: M 300 THR cc_start: 0.6194 (OUTLIER) cc_final: 0.5909 (p) REVERT: M 345 ASN cc_start: 0.6212 (OUTLIER) cc_final: 0.5742 (t0) REVERT: M 407 MET cc_start: 0.2539 (OUTLIER) cc_final: 0.2011 (tmm) REVERT: M 433 GLU cc_start: 0.6260 (OUTLIER) cc_final: 0.5824 (mt-10) REVERT: N 211 ARG cc_start: 0.5658 (ttt180) cc_final: 0.4878 (ptm160) REVERT: N 238 LEU cc_start: 0.4994 (OUTLIER) cc_final: 0.4537 (tp) REVERT: N 407 MET cc_start: 0.2903 (ttp) cc_final: 0.2564 (tmm) REVERT: N 429 MET cc_start: 0.5797 (mmm) cc_final: 0.5546 (mmm) REVERT: N 433 GLU cc_start: 0.5534 (pp20) cc_final: 0.5249 (mt-10) REVERT: N 579 ASN cc_start: 0.7599 (t0) cc_final: 0.7242 (t0) REVERT: O 211 ARG cc_start: 0.5748 (ttt180) cc_final: 0.5468 (ttm170) REVERT: O 312 MET cc_start: 0.7543 (tpp) cc_final: 0.7234 (mmm) REVERT: O 365 PRO cc_start: 0.7324 (Cg_endo) cc_final: 0.6963 (Cg_exo) REVERT: O 407 MET cc_start: 0.2228 (tmm) cc_final: 0.2017 (tmm) REVERT: O 429 MET cc_start: 0.5495 (mmm) cc_final: 0.5261 (mmm) REVERT: O 433 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6089 (mt-10) REVERT: O 579 ASN cc_start: 0.7148 (t0) cc_final: 0.6880 (t0) outliers start: 221 outliers final: 150 residues processed: 818 average time/residue: 0.4790 time to fit residues: 684.4120 Evaluate side-chains 774 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 598 time to evaluate : 4.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 301 ASN Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 573 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 336 VAL Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 475 GLN Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 433 GLU Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 554 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 345 ASN Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 345 ASN Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 573 THR Chi-restraints excluded: chain L residue 613 VAL Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 345 ASN Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 587 ASN Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 342 ASP Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 423 THR Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 631 optimal weight: 9.9990 chunk 664 optimal weight: 6.9990 chunk 606 optimal weight: 0.9980 chunk 646 optimal weight: 10.0000 chunk 389 optimal weight: 6.9990 chunk 281 optimal weight: 9.9990 chunk 507 optimal weight: 9.9990 chunk 198 optimal weight: 0.9990 chunk 584 optimal weight: 0.0980 chunk 611 optimal weight: 3.9990 chunk 644 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 488 GLN E 533 GLN F 233 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 ASN ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 440 GLN K 496 GLN ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 587 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3293 moved from start: 0.6564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 55485 Z= 0.225 Angle : 0.679 13.133 75255 Z= 0.338 Chirality : 0.046 0.386 9120 Planarity : 0.005 0.105 9855 Dihedral : 5.573 46.335 7787 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.49 % Favored : 94.25 % Rotamer: Outliers : 3.56 % Allowed : 24.70 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.10), residues: 7200 helix: 0.60 (0.11), residues: 2055 sheet: -0.98 (0.10), residues: 2700 loop : -2.04 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 405 HIS 0.003 0.001 HIS H 133 PHE 0.016 0.002 PHE M 507 TYR 0.035 0.002 TYR L 174 ARG 0.006 0.000 ARG J 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 615 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.6861 (OUTLIER) cc_final: 0.6631 (t0) REVERT: A 365 PRO cc_start: 0.7215 (Cg_endo) cc_final: 0.6838 (Cg_exo) REVERT: A 433 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6164 (tm-30) REVERT: B 345 ASN cc_start: 0.6272 (OUTLIER) cc_final: 0.5726 (t0) REVERT: B 413 SER cc_start: 0.5534 (m) cc_final: 0.5015 (t) REVERT: B 433 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6371 (mt-10) REVERT: B 593 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6802 (ttm-80) REVERT: C 211 ARG cc_start: 0.6348 (ttt180) cc_final: 0.5681 (ptm160) REVERT: C 238 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5265 (tp) REVERT: C 345 ASN cc_start: 0.6513 (OUTLIER) cc_final: 0.6129 (t0) REVERT: C 365 PRO cc_start: 0.7379 (Cg_endo) cc_final: 0.7082 (Cg_exo) REVERT: C 413 SER cc_start: 0.5550 (m) cc_final: 0.4830 (t) REVERT: C 433 GLU cc_start: 0.6882 (pt0) cc_final: 0.6556 (mt-10) REVERT: C 579 ASN cc_start: 0.7525 (t0) cc_final: 0.7187 (t0) REVERT: C 593 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.7107 (ttt90) REVERT: D 182 ARG cc_start: 0.6304 (ttm110) cc_final: 0.6063 (mtm-85) REVERT: D 238 LEU cc_start: 0.5083 (OUTLIER) cc_final: 0.4573 (tt) REVERT: D 312 MET cc_start: 0.7387 (tpp) cc_final: 0.6900 (tpp) REVERT: D 345 ASN cc_start: 0.6415 (OUTLIER) cc_final: 0.5969 (t0) REVERT: D 365 PRO cc_start: 0.7154 (Cg_endo) cc_final: 0.6799 (Cg_exo) REVERT: D 407 MET cc_start: 0.2578 (tmm) cc_final: 0.2044 (tmm) REVERT: D 413 SER cc_start: 0.4815 (m) cc_final: 0.4232 (t) REVERT: D 433 GLU cc_start: 0.6352 (OUTLIER) cc_final: 0.5930 (mt-10) REVERT: D 579 ASN cc_start: 0.7548 (t0) cc_final: 0.7259 (t0) REVERT: D 591 LEU cc_start: 0.8551 (mt) cc_final: 0.8259 (tp) REVERT: E 160 ASP cc_start: 0.4379 (t70) cc_final: 0.4076 (m-30) REVERT: E 365 PRO cc_start: 0.7725 (Cg_endo) cc_final: 0.7463 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.5443 (mt-10) REVERT: E 478 GLU cc_start: 0.6984 (tp30) cc_final: 0.6570 (pp20) REVERT: E 481 SER cc_start: 0.5105 (m) cc_final: 0.4854 (p) REVERT: F 100 MET cc_start: 0.2845 (mmt) cc_final: 0.2591 (mmm) REVERT: F 160 ASP cc_start: 0.6355 (t70) cc_final: 0.5958 (t0) REVERT: F 230 MET cc_start: 0.6182 (mmt) cc_final: 0.5976 (tmm) REVERT: F 312 MET cc_start: 0.7744 (tpt) cc_final: 0.7219 (mmm) REVERT: F 358 THR cc_start: 0.3540 (OUTLIER) cc_final: 0.3009 (p) REVERT: F 433 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.6037 (mt-10) REVERT: F 579 ASN cc_start: 0.7265 (t0) cc_final: 0.6983 (t0) REVERT: G 160 ASP cc_start: 0.6347 (t70) cc_final: 0.5867 (t70) REVERT: G 180 MET cc_start: 0.7077 (mmm) cc_final: 0.6787 (mmm) REVERT: G 407 MET cc_start: 0.3360 (tmm) cc_final: 0.3126 (tmm) REVERT: G 433 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6631 (mt-10) REVERT: G 579 ASN cc_start: 0.7444 (t0) cc_final: 0.7137 (t0) REVERT: H 100 MET cc_start: 0.1546 (ttt) cc_final: 0.0075 (mtp) REVERT: H 316 GLU cc_start: 0.7814 (tt0) cc_final: 0.7406 (tm-30) REVERT: H 345 ASN cc_start: 0.6584 (OUTLIER) cc_final: 0.6205 (t0) REVERT: H 407 MET cc_start: 0.4284 (ttp) cc_final: 0.3788 (tmm) REVERT: H 433 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5989 (mt-10) REVERT: H 579 ASN cc_start: 0.7301 (t0) cc_final: 0.6928 (t0) REVERT: I 478 GLU cc_start: 0.7635 (tp30) cc_final: 0.7276 (pp20) REVERT: J 238 LEU cc_start: 0.5908 (OUTLIER) cc_final: 0.5508 (tp) REVERT: J 345 ASN cc_start: 0.6487 (OUTLIER) cc_final: 0.6229 (t0) REVERT: J 433 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6558 (mt-10) REVERT: J 593 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7106 (ttm-80) REVERT: K 312 MET cc_start: 0.7253 (tpp) cc_final: 0.6833 (tpp) REVERT: K 316 GLU cc_start: 0.7889 (tt0) cc_final: 0.7485 (tm-30) REVERT: K 579 ASN cc_start: 0.7176 (t0) cc_final: 0.6850 (t0) REVERT: L 211 ARG cc_start: 0.5789 (mtt180) cc_final: 0.5448 (ptm-80) REVERT: L 251 TYR cc_start: 0.5083 (m-80) cc_final: 0.4870 (m-80) REVERT: L 345 ASN cc_start: 0.6481 (OUTLIER) cc_final: 0.5982 (t0) REVERT: L 407 MET cc_start: 0.3035 (tmm) cc_final: 0.2799 (tmm) REVERT: L 433 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6613 (mt-10) REVERT: L 550 LEU cc_start: 0.7105 (mt) cc_final: 0.6807 (tp) REVERT: M 300 THR cc_start: 0.6303 (OUTLIER) cc_final: 0.6053 (p) REVERT: M 345 ASN cc_start: 0.6225 (OUTLIER) cc_final: 0.5755 (t0) REVERT: M 407 MET cc_start: 0.2480 (OUTLIER) cc_final: 0.1999 (tmm) REVERT: M 433 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5889 (mt-10) REVERT: N 211 ARG cc_start: 0.5845 (ttt180) cc_final: 0.5056 (ptm160) REVERT: N 238 LEU cc_start: 0.5028 (OUTLIER) cc_final: 0.4550 (tp) REVERT: N 345 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6093 (t0) REVERT: N 407 MET cc_start: 0.2555 (ttp) cc_final: 0.2273 (tmm) REVERT: N 429 MET cc_start: 0.5795 (mmm) cc_final: 0.5544 (mmm) REVERT: N 433 GLU cc_start: 0.5697 (pp20) cc_final: 0.5350 (mt-10) REVERT: N 579 ASN cc_start: 0.7604 (t0) cc_final: 0.7251 (t0) REVERT: O 211 ARG cc_start: 0.6002 (ttt180) cc_final: 0.5644 (ttm170) REVERT: O 312 MET cc_start: 0.7432 (tpp) cc_final: 0.7088 (mmm) REVERT: O 365 PRO cc_start: 0.7380 (Cg_endo) cc_final: 0.6986 (Cg_exo) REVERT: O 407 MET cc_start: 0.2351 (tmm) cc_final: 0.2136 (tmm) REVERT: O 429 MET cc_start: 0.5396 (mmm) cc_final: 0.5090 (mmm) REVERT: O 433 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6104 (mt-10) REVERT: O 591 LEU cc_start: 0.8907 (mt) cc_final: 0.8657 (tp) outliers start: 215 outliers final: 165 residues processed: 768 average time/residue: 0.4908 time to fit residues: 654.5474 Evaluate side-chains 788 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 594 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 613 VAL Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 573 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 257 MET Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain H residue 171 LYS Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 475 GLN Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 554 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 345 ASN Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 593 ARG Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 345 ASN Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 476 ILE Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 573 THR Chi-restraints excluded: chain L residue 613 VAL Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 345 ASN Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 587 ASN Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 342 ASP Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 423 THR Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 424 optimal weight: 5.9990 chunk 683 optimal weight: 0.2980 chunk 417 optimal weight: 0.0000 chunk 324 optimal weight: 20.0000 chunk 475 optimal weight: 4.9990 chunk 717 optimal weight: 9.9990 chunk 660 optimal weight: 9.9990 chunk 571 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 441 optimal weight: 0.9980 chunk 350 optimal weight: 6.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN F 233 GLN ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 587 ASN ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3296 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 55485 Z= 0.257 Angle : 0.694 12.332 75255 Z= 0.347 Chirality : 0.047 0.388 9120 Planarity : 0.005 0.099 9855 Dihedral : 5.625 45.326 7787 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.18 % Favored : 93.56 % Rotamer: Outliers : 3.44 % Allowed : 24.76 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.10), residues: 7200 helix: 0.62 (0.11), residues: 2055 sheet: -0.97 (0.10), residues: 2610 loop : -2.11 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 405 HIS 0.002 0.001 HIS G 133 PHE 0.027 0.002 PHE J 592 TYR 0.031 0.002 TYR M 174 ARG 0.010 0.000 ARG H 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14400 Ramachandran restraints generated. 7200 Oldfield, 0 Emsley, 7200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 615 time to evaluate : 4.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASN cc_start: 0.6693 (OUTLIER) cc_final: 0.6482 (t0) REVERT: A 365 PRO cc_start: 0.7251 (Cg_endo) cc_final: 0.6883 (Cg_exo) REVERT: A 433 GLU cc_start: 0.6604 (mt-10) cc_final: 0.6271 (tm-30) REVERT: B 345 ASN cc_start: 0.6280 (OUTLIER) cc_final: 0.5733 (t0) REVERT: B 413 SER cc_start: 0.5523 (m) cc_final: 0.4976 (t) REVERT: B 433 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6359 (mt-10) REVERT: B 593 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6811 (ttt-90) REVERT: C 211 ARG cc_start: 0.6364 (ttt180) cc_final: 0.5699 (ptm160) REVERT: C 238 LEU cc_start: 0.5666 (OUTLIER) cc_final: 0.5138 (tp) REVERT: C 345 ASN cc_start: 0.6522 (OUTLIER) cc_final: 0.6141 (t0) REVERT: C 365 PRO cc_start: 0.7391 (Cg_endo) cc_final: 0.7094 (Cg_exo) REVERT: C 413 SER cc_start: 0.5534 (m) cc_final: 0.4785 (t) REVERT: C 433 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6595 (mt-10) REVERT: C 579 ASN cc_start: 0.7509 (t0) cc_final: 0.7179 (t0) REVERT: C 593 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.7126 (ttt90) REVERT: D 180 MET cc_start: 0.6792 (mtt) cc_final: 0.6317 (mtm) REVERT: D 238 LEU cc_start: 0.5175 (OUTLIER) cc_final: 0.4720 (tt) REVERT: D 251 TYR cc_start: 0.5215 (m-80) cc_final: 0.4821 (m-80) REVERT: D 312 MET cc_start: 0.7364 (tpp) cc_final: 0.6882 (tpp) REVERT: D 345 ASN cc_start: 0.6454 (OUTLIER) cc_final: 0.5984 (t0) REVERT: D 358 THR cc_start: 0.3546 (OUTLIER) cc_final: 0.3037 (p) REVERT: D 365 PRO cc_start: 0.7168 (Cg_endo) cc_final: 0.6808 (Cg_exo) REVERT: D 407 MET cc_start: 0.2774 (tmm) cc_final: 0.2233 (tmm) REVERT: D 413 SER cc_start: 0.4653 (m) cc_final: 0.3965 (t) REVERT: D 433 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5903 (mt-10) REVERT: D 579 ASN cc_start: 0.7567 (t0) cc_final: 0.7283 (t0) REVERT: E 160 ASP cc_start: 0.4390 (t70) cc_final: 0.4074 (m-30) REVERT: E 316 GLU cc_start: 0.7716 (tt0) cc_final: 0.7234 (tm-30) REVERT: E 365 PRO cc_start: 0.7728 (Cg_endo) cc_final: 0.7480 (Cg_exo) REVERT: E 433 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.5455 (mt-10) REVERT: E 478 GLU cc_start: 0.6970 (tp30) cc_final: 0.6554 (pp20) REVERT: F 100 MET cc_start: 0.2868 (mmt) cc_final: 0.2614 (mmm) REVERT: F 160 ASP cc_start: 0.6259 (t70) cc_final: 0.5852 (t0) REVERT: F 211 ARG cc_start: 0.6566 (mtt180) cc_final: 0.5981 (ptm160) REVERT: F 312 MET cc_start: 0.7596 (tpt) cc_final: 0.7159 (tpp) REVERT: F 358 THR cc_start: 0.3593 (OUTLIER) cc_final: 0.3056 (p) REVERT: F 433 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.6035 (mt-10) REVERT: F 579 ASN cc_start: 0.7362 (t0) cc_final: 0.7074 (t0) REVERT: G 160 ASP cc_start: 0.6353 (t70) cc_final: 0.5875 (t70) REVERT: G 180 MET cc_start: 0.6835 (mmm) cc_final: 0.6452 (mmm) REVERT: G 407 MET cc_start: 0.3298 (tmm) cc_final: 0.3033 (tmm) REVERT: G 433 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: G 579 ASN cc_start: 0.7401 (t0) cc_final: 0.7078 (t0) REVERT: H 100 MET cc_start: 0.1548 (ttt) cc_final: 0.0067 (mtp) REVERT: H 211 ARG cc_start: 0.6287 (ttt180) cc_final: 0.5447 (tpp80) REVERT: H 316 GLU cc_start: 0.7815 (tt0) cc_final: 0.7407 (tm-30) REVERT: H 345 ASN cc_start: 0.6594 (OUTLIER) cc_final: 0.6213 (t0) REVERT: H 407 MET cc_start: 0.4359 (ttp) cc_final: 0.3872 (tmm) REVERT: H 433 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.6002 (mt-10) REVERT: H 579 ASN cc_start: 0.7278 (t0) cc_final: 0.6915 (t0) REVERT: J 238 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5528 (tp) REVERT: J 345 ASN cc_start: 0.6497 (OUTLIER) cc_final: 0.6239 (t0) REVERT: J 433 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6546 (mt-10) REVERT: K 312 MET cc_start: 0.7255 (tpp) cc_final: 0.6840 (tpp) REVERT: K 316 GLU cc_start: 0.7886 (tt0) cc_final: 0.7486 (tm-30) REVERT: K 342 ASP cc_start: 0.5894 (OUTLIER) cc_final: 0.5691 (p0) REVERT: K 579 ASN cc_start: 0.7319 (t0) cc_final: 0.7030 (t0) REVERT: L 211 ARG cc_start: 0.5863 (mtt180) cc_final: 0.5517 (ptm160) REVERT: L 251 TYR cc_start: 0.5062 (m-80) cc_final: 0.4852 (m-80) REVERT: L 345 ASN cc_start: 0.6473 (OUTLIER) cc_final: 0.5962 (t0) REVERT: L 407 MET cc_start: 0.3362 (tmm) cc_final: 0.3160 (tmm) REVERT: L 433 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6498 (mt-10) REVERT: M 300 THR cc_start: 0.6315 (OUTLIER) cc_final: 0.6061 (p) REVERT: M 345 ASN cc_start: 0.6259 (OUTLIER) cc_final: 0.5780 (t0) REVERT: M 407 MET cc_start: 0.2763 (OUTLIER) cc_final: 0.2459 (tmm) REVERT: M 433 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5922 (mt-10) REVERT: N 211 ARG cc_start: 0.5919 (ttt180) cc_final: 0.5036 (ptm160) REVERT: N 238 LEU cc_start: 0.4954 (OUTLIER) cc_final: 0.4513 (tp) REVERT: N 345 ASN cc_start: 0.6462 (OUTLIER) cc_final: 0.5826 (t0) REVERT: N 407 MET cc_start: 0.2669 (ttp) cc_final: 0.2395 (tmm) REVERT: N 429 MET cc_start: 0.5800 (mmm) cc_final: 0.5556 (mmm) REVERT: N 433 GLU cc_start: 0.5875 (pp20) cc_final: 0.5549 (mt-10) REVERT: N 579 ASN cc_start: 0.7616 (t0) cc_final: 0.7259 (t0) REVERT: O 211 ARG cc_start: 0.6159 (ttt180) cc_final: 0.5808 (ttm170) REVERT: O 312 MET cc_start: 0.7540 (tpp) cc_final: 0.7172 (mmm) REVERT: O 365 PRO cc_start: 0.7393 (Cg_endo) cc_final: 0.6995 (Cg_exo) REVERT: O 376 ASP cc_start: 0.5847 (m-30) cc_final: 0.5610 (p0) REVERT: O 407 MET cc_start: 0.2487 (tmm) cc_final: 0.2275 (tmm) REVERT: O 429 MET cc_start: 0.5299 (mmm) cc_final: 0.4997 (mmm) REVERT: O 433 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6097 (mt-10) outliers start: 208 outliers final: 168 residues processed: 765 average time/residue: 0.4820 time to fit residues: 642.6729 Evaluate side-chains 792 residues out of total 6045 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 593 time to evaluate : 4.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 345 ASN Chi-restraints excluded: chain A residue 350 TRP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 425 SER Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 509 THR Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 433 GLU Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 473 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain B residue 534 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 593 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 433 GLU Chi-restraints excluded: chain C residue 460 THR Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 541 VAL Chi-restraints excluded: chain C residue 593 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 257 MET Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 336 VAL Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 358 THR Chi-restraints excluded: chain D residue 416 THR Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 433 GLU Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 512 VAL Chi-restraints excluded: chain D residue 541 VAL Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 217 VAL Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 329 VAL Chi-restraints excluded: chain E residue 337 GLU Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain E residue 460 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 503 LEU Chi-restraints excluded: chain E residue 529 LEU Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 350 TRP Chi-restraints excluded: chain F residue 358 THR Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain F residue 433 GLU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 573 THR Chi-restraints excluded: chain G residue 134 TYR Chi-restraints excluded: chain G residue 207 VAL Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 329 VAL Chi-restraints excluded: chain G residue 336 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 416 THR Chi-restraints excluded: chain G residue 423 THR Chi-restraints excluded: chain G residue 433 GLU Chi-restraints excluded: chain G residue 460 THR Chi-restraints excluded: chain G residue 473 THR Chi-restraints excluded: chain G residue 509 THR Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 300 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 329 VAL Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain H residue 416 THR Chi-restraints excluded: chain H residue 423 THR Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 460 THR Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 475 GLN Chi-restraints excluded: chain H residue 529 LEU Chi-restraints excluded: chain H residue 613 VAL Chi-restraints excluded: chain I residue 244 THR Chi-restraints excluded: chain I residue 257 MET Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 300 THR Chi-restraints excluded: chain I residue 329 VAL Chi-restraints excluded: chain I residue 394 ASN Chi-restraints excluded: chain I residue 423 THR Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 554 PHE Chi-restraints excluded: chain J residue 181 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 238 LEU Chi-restraints excluded: chain J residue 257 MET Chi-restraints excluded: chain J residue 300 THR Chi-restraints excluded: chain J residue 329 VAL Chi-restraints excluded: chain J residue 336 VAL Chi-restraints excluded: chain J residue 342 ASP Chi-restraints excluded: chain J residue 345 ASN Chi-restraints excluded: chain J residue 433 GLU Chi-restraints excluded: chain J residue 460 THR Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 529 LEU Chi-restraints excluded: chain J residue 613 VAL Chi-restraints excluded: chain K residue 215 VAL Chi-restraints excluded: chain K residue 298 GLU Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 329 VAL Chi-restraints excluded: chain K residue 342 ASP Chi-restraints excluded: chain K residue 425 SER Chi-restraints excluded: chain K residue 460 THR Chi-restraints excluded: chain K residue 473 THR Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 613 VAL Chi-restraints excluded: chain L residue 181 VAL Chi-restraints excluded: chain L residue 257 MET Chi-restraints excluded: chain L residue 300 THR Chi-restraints excluded: chain L residue 306 THR Chi-restraints excluded: chain L residue 329 VAL Chi-restraints excluded: chain L residue 336 VAL Chi-restraints excluded: chain L residue 345 ASN Chi-restraints excluded: chain L residue 433 GLU Chi-restraints excluded: chain L residue 473 THR Chi-restraints excluded: chain L residue 529 LEU Chi-restraints excluded: chain L residue 573 THR Chi-restraints excluded: chain L residue 613 VAL Chi-restraints excluded: chain M residue 181 VAL Chi-restraints excluded: chain M residue 182 ARG Chi-restraints excluded: chain M residue 257 MET Chi-restraints excluded: chain M residue 300 THR Chi-restraints excluded: chain M residue 306 THR Chi-restraints excluded: chain M residue 329 VAL Chi-restraints excluded: chain M residue 336 VAL Chi-restraints excluded: chain M residue 345 ASN Chi-restraints excluded: chain M residue 407 MET Chi-restraints excluded: chain M residue 416 THR Chi-restraints excluded: chain M residue 431 ASN Chi-restraints excluded: chain M residue 433 GLU Chi-restraints excluded: chain M residue 460 THR Chi-restraints excluded: chain M residue 473 THR Chi-restraints excluded: chain M residue 529 LEU Chi-restraints excluded: chain M residue 587 ASN Chi-restraints excluded: chain M residue 613 VAL Chi-restraints excluded: chain N residue 181 VAL Chi-restraints excluded: chain N residue 217 VAL Chi-restraints excluded: chain N residue 238 LEU Chi-restraints excluded: chain N residue 329 VAL Chi-restraints excluded: chain N residue 342 ASP Chi-restraints excluded: chain N residue 345 ASN Chi-restraints excluded: chain N residue 425 SER Chi-restraints excluded: chain N residue 460 THR Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 529 LEU Chi-restraints excluded: chain O residue 181 VAL Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 300 THR Chi-restraints excluded: chain O residue 306 THR Chi-restraints excluded: chain O residue 329 VAL Chi-restraints excluded: chain O residue 336 VAL Chi-restraints excluded: chain O residue 350 TRP Chi-restraints excluded: chain O residue 416 THR Chi-restraints excluded: chain O residue 423 THR Chi-restraints excluded: chain O residue 433 GLU Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 473 THR Chi-restraints excluded: chain O residue 529 LEU Chi-restraints excluded: chain O residue 613 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 720 random chunks: chunk 453 optimal weight: 9.9990 chunk 608 optimal weight: 0.0670 chunk 174 optimal weight: 0.8980 chunk 526 optimal weight: 0.8980 chunk 84 optimal weight: 0.0870 chunk 158 optimal weight: 9.9990 chunk 572 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 587 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 GLN ** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 GLN ** E 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 595 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 440 GLN ** L 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 565 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.227598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.212717 restraints weight = 70623.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.208531 restraints weight = 114852.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.205894 restraints weight = 73436.990| |-----------------------------------------------------------------------------| r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 55485 Z= 0.174 Angle : 0.650 12.499 75255 Z= 0.322 Chirality : 0.046 0.464 9120 Planarity : 0.004 0.085 9855 Dihedral : 5.321 42.129 7787 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.86 % Favored : 95.88 % Rotamer: Outliers : 3.03 % Allowed : 25.11 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.10), residues: 7200 helix: 0.77 (0.11), residues: 2055 sheet: -0.73 (0.10), residues: 2700 loop : -1.92 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 405 HIS 0.003 0.001 HIS G 133 PHE 0.025 0.001 PHE J 592 TYR 0.027 0.002 TYR M 174 ARG 0.006 0.000 ARG J 224 =============================================================================== Job complete usr+sys time: 12524.24 seconds wall clock time: 221 minutes 8.79 seconds (13268.79 seconds total)