Starting phenix.real_space_refine on Sun Mar 17 11:09:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn7_34156/03_2024/8gn7_34156_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn7_34156/03_2024/8gn7_34156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn7_34156/03_2024/8gn7_34156.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn7_34156/03_2024/8gn7_34156.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn7_34156/03_2024/8gn7_34156_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gn7_34156/03_2024/8gn7_34156_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 140 5.16 5 C 11900 2.51 5 N 2710 2.21 5 O 2760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 47": "OD1" <-> "OD2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 138": "OD1" <-> "OD2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "J PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 138": "OD1" <-> "OD2" Residue "J GLU 154": "OE1" <-> "OE2" Residue "J GLU 193": "OE1" <-> "OE2" Residue "M ASP 47": "OD1" <-> "OD2" Residue "M PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 138": "OD1" <-> "OD2" Residue "M ASP 185": "OD1" <-> "OD2" Residue "M ASP 215": "OD1" <-> "OD2" Residue "P PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 47": "OD1" <-> "OD2" Residue "P GLU 50": "OE1" <-> "OE2" Residue "P PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 138": "OD1" <-> "OD2" Residue "P ASP 185": "OD1" <-> "OD2" Residue "P ASP 215": "OD1" <-> "OD2" Residue "S PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 47": "OD1" <-> "OD2" Residue "S GLU 48": "OE1" <-> "OE2" Residue "S PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 138": "OD1" <-> "OD2" Residue "V ASP 47": "OD1" <-> "OD2" Residue "V GLU 50": "OE1" <-> "OE2" Residue "V PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 138": "OD1" <-> "OD2" Residue "V GLU 154": "OE1" <-> "OE2" Residue "Y ASP 47": "OD1" <-> "OD2" Residue "Y GLU 50": "OE1" <-> "OE2" Residue "Y PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 138": "OD1" <-> "OD2" Residue "Y ASP 185": "OD1" <-> "OD2" Residue "Y ASP 215": "OD1" <-> "OD2" Residue "b ASP 47": "OD1" <-> "OD2" Residue "b PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 138": "OD1" <-> "OD2" Residue "b GLU 154": "OE1" <-> "OE2" Residue "b ASP 185": "OD1" <-> "OD2" Residue "b ASP 215": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17530 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "B" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "G" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "J" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "M" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "P" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "S" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "V" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "Y" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "b" Number of atoms: 1588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1588 Classifications: {'peptide': 203} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 190} Chain breaks: 1 Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3PE': 1, 'CLR': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "B" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3PE': 1, 'CLR': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "G" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3PE': 1, 'CLR': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "J" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "M" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 193 Unusual residues: {'3PE': 1, 'CLR': 4, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "P" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "S" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 193 Unusual residues: {'3PE': 1, 'CLR': 4, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "V" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'3PE': 1, 'CLR': 2, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "Y" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 193 Unusual residues: {'3PE': 1, 'CLR': 4, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Chain: "b" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 165 Unusual residues: {'3PE': 1, 'CLR': 3, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Time building chain proxies: 9.40, per 1000 atoms: 0.54 Number of scatterers: 17530 At special positions: 0 Unit cell: (92.92, 91.08, 179.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 20 15.00 O 2760 8.00 N 2710 7.00 C 11900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 186 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 186 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 175 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 186 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 180 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 175 " distance=2.03 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 186 " distance=2.03 Simple disulfide: pdb=" SG CYS M 61 " - pdb=" SG CYS M 180 " distance=2.03 Simple disulfide: pdb=" SG CYS M 65 " - pdb=" SG CYS M 175 " distance=2.03 Simple disulfide: pdb=" SG CYS P 54 " - pdb=" SG CYS P 186 " distance=2.03 Simple disulfide: pdb=" SG CYS P 61 " - pdb=" SG CYS P 180 " distance=2.03 Simple disulfide: pdb=" SG CYS P 65 " - pdb=" SG CYS P 175 " distance=2.03 Simple disulfide: pdb=" SG CYS S 54 " - pdb=" SG CYS S 186 " distance=2.03 Simple disulfide: pdb=" SG CYS S 61 " - pdb=" SG CYS S 180 " distance=2.03 Simple disulfide: pdb=" SG CYS S 65 " - pdb=" SG CYS S 175 " distance=2.03 Simple disulfide: pdb=" SG CYS V 54 " - pdb=" SG CYS V 186 " distance=2.03 Simple disulfide: pdb=" SG CYS V 61 " - pdb=" SG CYS V 180 " distance=2.03 Simple disulfide: pdb=" SG CYS V 65 " - pdb=" SG CYS V 175 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 186 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 61 " - pdb=" SG CYS Y 180 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 65 " - pdb=" SG CYS Y 175 " distance=2.03 Simple disulfide: pdb=" SG CYS b 54 " - pdb=" SG CYS b 186 " distance=2.03 Simple disulfide: pdb=" SG CYS b 61 " - pdb=" SG CYS b 180 " distance=2.03 Simple disulfide: pdb=" SG CYS b 65 " - pdb=" SG CYS b 175 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.85 Conformation dependent library (CDL) restraints added in 2.4 seconds 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 10 sheets defined 58.3% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 9 through 12 No H-bonds generated for 'chain 'A' and resid 9 through 12' Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.598A pdb=" N MET A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.834A pdb=" N VAL A 38 " --> pdb=" O MET A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 74 through 85 removed outlier: 3.525A pdb=" N VAL A 85 " --> pdb=" O GLN A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 101 removed outlier: 3.540A pdb=" N PHE A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 165 removed outlier: 3.959A pdb=" N ILE A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 225 removed outlier: 3.627A pdb=" N LEU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 211 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 213 " --> pdb=" O PHE A 209 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG A 221 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 12 No H-bonds generated for 'chain 'B' and resid 9 through 12' Processing helix chain 'B' and resid 20 through 31 removed outlier: 3.641A pdb=" N MET B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.846A pdb=" N VAL B 38 " --> pdb=" O MET B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 74 through 85 removed outlier: 3.518A pdb=" N VAL B 85 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 101 removed outlier: 3.573A pdb=" N PHE B 92 " --> pdb=" O PRO B 88 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 165 removed outlier: 4.034A pdb=" N ILE B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 157 " --> pdb=" O LEU B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 225 removed outlier: 3.606A pdb=" N LEU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B 210 " --> pdb=" O ALA B 206 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 213 " --> pdb=" O PHE B 209 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL B 217 " --> pdb=" O LEU B 213 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 221 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 12 No H-bonds generated for 'chain 'G' and resid 9 through 12' Processing helix chain 'G' and resid 14 through 16 No H-bonds generated for 'chain 'G' and resid 14 through 16' Processing helix chain 'G' and resid 20 through 31 removed outlier: 3.539A pdb=" N VAL G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET G 30 " --> pdb=" O PHE G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 39 removed outlier: 3.835A pdb=" N VAL G 38 " --> pdb=" O MET G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 74 through 85 removed outlier: 3.508A pdb=" N VAL G 85 " --> pdb=" O GLN G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.584A pdb=" N PHE G 92 " --> pdb=" O PRO G 88 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER G 93 " --> pdb=" O SER G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 164 removed outlier: 3.966A pdb=" N ILE G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS G 146 " --> pdb=" O GLY G 142 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA G 155 " --> pdb=" O THR G 151 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 157 " --> pdb=" O LEU G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 225 removed outlier: 3.596A pdb=" N LEU G 199 " --> pdb=" O SER G 195 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 210 " --> pdb=" O ALA G 206 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU G 213 " --> pdb=" O PHE G 209 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N CYS G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG G 221 " --> pdb=" O VAL G 217 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG G 225 " --> pdb=" O ARG G 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 12 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 20 through 31 removed outlier: 3.791A pdb=" N MET J 30 " --> pdb=" O PHE J 26 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU J 31 " --> pdb=" O VAL J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 39 removed outlier: 3.852A pdb=" N VAL J 38 " --> pdb=" O MET J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 69 Processing helix chain 'J' and resid 74 through 101 removed outlier: 3.506A pdb=" N VAL J 85 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) Proline residue: J 88 - end of helix removed outlier: 3.590A pdb=" N PHE J 92 " --> pdb=" O PRO J 88 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER J 93 " --> pdb=" O SER J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 164 removed outlier: 3.965A pdb=" N ILE J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N HIS J 146 " --> pdb=" O GLY J 142 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU J 154 " --> pdb=" O ARG J 150 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA J 155 " --> pdb=" O THR J 151 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 225 removed outlier: 3.626A pdb=" N LEU J 199 " --> pdb=" O SER J 195 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU J 210 " --> pdb=" O ALA J 206 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU J 211 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY J 212 " --> pdb=" O SER J 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU J 213 " --> pdb=" O PHE J 209 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL J 217 " --> pdb=" O LEU J 213 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS J 218 " --> pdb=" O ALA J 214 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG J 221 " --> pdb=" O VAL J 217 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG J 225 " --> pdb=" O ARG J 221 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 12 No H-bonds generated for 'chain 'M' and resid 9 through 12' Processing helix chain 'M' and resid 14 through 16 No H-bonds generated for 'chain 'M' and resid 14 through 16' Processing helix chain 'M' and resid 20 through 31 removed outlier: 3.809A pdb=" N MET M 30 " --> pdb=" O PHE M 26 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU M 31 " --> pdb=" O VAL M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 34 through 39 removed outlier: 3.809A pdb=" N VAL M 38 " --> pdb=" O MET M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 69 Processing helix chain 'M' and resid 74 through 85 Processing helix chain 'M' and resid 87 through 101 removed outlier: 3.556A pdb=" N PHE M 92 " --> pdb=" O PRO M 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER M 93 " --> pdb=" O SER M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 165 removed outlier: 3.963A pdb=" N ILE M 145 " --> pdb=" O ALA M 141 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS M 146 " --> pdb=" O GLY M 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA M 155 " --> pdb=" O THR M 151 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE M 157 " --> pdb=" O LEU M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 225 removed outlier: 3.597A pdb=" N LEU M 199 " --> pdb=" O SER M 195 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU M 210 " --> pdb=" O ALA M 206 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU M 211 " --> pdb=" O LEU M 207 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU M 213 " --> pdb=" O PHE M 209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL M 217 " --> pdb=" O LEU M 213 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N CYS M 218 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG M 221 " --> pdb=" O VAL M 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG M 225 " --> pdb=" O ARG M 221 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 12 No H-bonds generated for 'chain 'P' and resid 9 through 12' Processing helix chain 'P' and resid 20 through 31 removed outlier: 3.584A pdb=" N MET P 30 " --> pdb=" O PHE P 26 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU P 31 " --> pdb=" O VAL P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 39 removed outlier: 3.839A pdb=" N VAL P 38 " --> pdb=" O MET P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 69 Processing helix chain 'P' and resid 74 through 85 removed outlier: 3.513A pdb=" N VAL P 85 " --> pdb=" O GLN P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 101 removed outlier: 3.566A pdb=" N PHE P 92 " --> pdb=" O PRO P 88 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER P 93 " --> pdb=" O SER P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 165 removed outlier: 4.045A pdb=" N ILE P 145 " --> pdb=" O ALA P 141 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N HIS P 146 " --> pdb=" O GLY P 142 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU P 154 " --> pdb=" O ARG P 150 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA P 155 " --> pdb=" O THR P 151 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA P 156 " --> pdb=" O LEU P 152 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE P 157 " --> pdb=" O LEU P 153 " (cutoff:3.500A) Processing helix chain 'P' and resid 193 through 225 removed outlier: 3.601A pdb=" N LEU P 199 " --> pdb=" O SER P 195 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU P 210 " --> pdb=" O ALA P 206 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU P 211 " --> pdb=" O LEU P 207 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY P 212 " --> pdb=" O SER P 208 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU P 213 " --> pdb=" O PHE P 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL P 217 " --> pdb=" O LEU P 213 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N CYS P 218 " --> pdb=" O ALA P 214 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG P 221 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG P 225 " --> pdb=" O ARG P 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 12 No H-bonds generated for 'chain 'S' and resid 9 through 12' Processing helix chain 'S' and resid 20 through 31 removed outlier: 3.536A pdb=" N MET S 30 " --> pdb=" O PHE S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 39 removed outlier: 3.842A pdb=" N VAL S 38 " --> pdb=" O MET S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 69 Processing helix chain 'S' and resid 74 through 85 removed outlier: 3.514A pdb=" N VAL S 85 " --> pdb=" O GLN S 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 101 removed outlier: 3.547A pdb=" N PHE S 92 " --> pdb=" O PRO S 88 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER S 93 " --> pdb=" O SER S 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 164 removed outlier: 3.967A pdb=" N ILE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS S 146 " --> pdb=" O GLY S 142 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA S 155 " --> pdb=" O THR S 151 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA S 156 " --> pdb=" O LEU S 152 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE S 157 " --> pdb=" O LEU S 153 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 225 removed outlier: 3.591A pdb=" N LEU S 199 " --> pdb=" O SER S 195 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE S 200 " --> pdb=" O LEU S 196 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU S 210 " --> pdb=" O ALA S 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU S 211 " --> pdb=" O LEU S 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY S 212 " --> pdb=" O SER S 208 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU S 213 " --> pdb=" O PHE S 209 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL S 217 " --> pdb=" O LEU S 213 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N CYS S 218 " --> pdb=" O ALA S 214 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG S 221 " --> pdb=" O VAL S 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG S 225 " --> pdb=" O ARG S 221 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 12 No H-bonds generated for 'chain 'V' and resid 9 through 12' Processing helix chain 'V' and resid 14 through 16 No H-bonds generated for 'chain 'V' and resid 14 through 16' Processing helix chain 'V' and resid 20 through 31 removed outlier: 3.781A pdb=" N MET V 30 " --> pdb=" O PHE V 26 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU V 31 " --> pdb=" O VAL V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 39 removed outlier: 3.848A pdb=" N VAL V 38 " --> pdb=" O MET V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 69 Processing helix chain 'V' and resid 74 through 85 removed outlier: 3.517A pdb=" N VAL V 85 " --> pdb=" O GLN V 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 101 removed outlier: 3.583A pdb=" N PHE V 92 " --> pdb=" O PRO V 88 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER V 93 " --> pdb=" O SER V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 141 through 165 removed outlier: 3.970A pdb=" N ILE V 145 " --> pdb=" O ALA V 141 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS V 146 " --> pdb=" O GLY V 142 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU V 154 " --> pdb=" O ARG V 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA V 155 " --> pdb=" O THR V 151 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA V 156 " --> pdb=" O LEU V 152 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N PHE V 157 " --> pdb=" O LEU V 153 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 225 removed outlier: 3.634A pdb=" N LEU V 199 " --> pdb=" O SER V 195 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU V 210 " --> pdb=" O ALA V 206 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU V 211 " --> pdb=" O LEU V 207 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY V 212 " --> pdb=" O SER V 208 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU V 213 " --> pdb=" O PHE V 209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL V 217 " --> pdb=" O LEU V 213 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N CYS V 218 " --> pdb=" O ALA V 214 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG V 221 " --> pdb=" O VAL V 217 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG V 225 " --> pdb=" O ARG V 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 12 No H-bonds generated for 'chain 'Y' and resid 9 through 12' Processing helix chain 'Y' and resid 14 through 16 No H-bonds generated for 'chain 'Y' and resid 14 through 16' Processing helix chain 'Y' and resid 20 through 31 removed outlier: 3.768A pdb=" N MET Y 30 " --> pdb=" O PHE Y 26 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU Y 31 " --> pdb=" O VAL Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 34 through 39 removed outlier: 3.817A pdb=" N VAL Y 38 " --> pdb=" O MET Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 69 Processing helix chain 'Y' and resid 74 through 85 Processing helix chain 'Y' and resid 87 through 101 removed outlier: 3.589A pdb=" N PHE Y 92 " --> pdb=" O PRO Y 88 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 164 removed outlier: 3.978A pdb=" N ILE Y 145 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS Y 146 " --> pdb=" O GLY Y 142 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA Y 155 " --> pdb=" O THR Y 151 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA Y 156 " --> pdb=" O LEU Y 152 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE Y 157 " --> pdb=" O LEU Y 153 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 225 removed outlier: 3.575A pdb=" N LEU Y 199 " --> pdb=" O SER Y 195 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Y 210 " --> pdb=" O ALA Y 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU Y 211 " --> pdb=" O LEU Y 207 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY Y 212 " --> pdb=" O SER Y 208 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU Y 213 " --> pdb=" O PHE Y 209 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL Y 217 " --> pdb=" O LEU Y 213 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N CYS Y 218 " --> pdb=" O ALA Y 214 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG Y 221 " --> pdb=" O VAL Y 217 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG Y 225 " --> pdb=" O ARG Y 221 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 12 No H-bonds generated for 'chain 'b' and resid 9 through 12' Processing helix chain 'b' and resid 14 through 16 No H-bonds generated for 'chain 'b' and resid 14 through 16' Processing helix chain 'b' and resid 20 through 31 removed outlier: 3.602A pdb=" N MET b 30 " --> pdb=" O PHE b 26 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU b 31 " --> pdb=" O VAL b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 34 through 39 removed outlier: 3.834A pdb=" N VAL b 38 " --> pdb=" O MET b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 41 through 44 No H-bonds generated for 'chain 'b' and resid 41 through 44' Processing helix chain 'b' and resid 61 through 69 Processing helix chain 'b' and resid 74 through 85 removed outlier: 3.516A pdb=" N VAL b 85 " --> pdb=" O GLN b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 101 removed outlier: 3.540A pdb=" N PHE b 92 " --> pdb=" O PRO b 88 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER b 93 " --> pdb=" O SER b 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 141 through 165 removed outlier: 3.984A pdb=" N ILE b 145 " --> pdb=" O ALA b 141 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS b 146 " --> pdb=" O GLY b 142 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA b 155 " --> pdb=" O THR b 151 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA b 156 " --> pdb=" O LEU b 152 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE b 157 " --> pdb=" O LEU b 153 " (cutoff:3.500A) Processing helix chain 'b' and resid 193 through 225 removed outlier: 3.609A pdb=" N LEU b 199 " --> pdb=" O SER b 195 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU b 211 " --> pdb=" O LEU b 207 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY b 212 " --> pdb=" O SER b 208 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU b 213 " --> pdb=" O PHE b 209 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL b 217 " --> pdb=" O LEU b 213 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N CYS b 218 " --> pdb=" O ALA b 214 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG b 221 " --> pdb=" O VAL b 217 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG b 225 " --> pdb=" O ARG b 221 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 172 through 175 Processing sheet with id= B, first strand: chain 'B' and resid 172 through 175 Processing sheet with id= C, first strand: chain 'G' and resid 172 through 175 Processing sheet with id= D, first strand: chain 'J' and resid 172 through 175 Processing sheet with id= E, first strand: chain 'M' and resid 172 through 175 Processing sheet with id= F, first strand: chain 'P' and resid 172 through 175 Processing sheet with id= G, first strand: chain 'S' and resid 172 through 175 Processing sheet with id= H, first strand: chain 'V' and resid 172 through 175 Processing sheet with id= I, first strand: chain 'Y' and resid 172 through 175 Processing sheet with id= J, first strand: chain 'b' and resid 172 through 175 677 hydrogen bonds defined for protein. 2001 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: 4.24 Time building geometry restraints manager: 6.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2630 1.33 - 1.45: 4410 1.45 - 1.57: 10730 1.57 - 1.69: 40 1.69 - 1.81: 190 Bond restraints: 18000 Sorted by residual: bond pdb=" CB ASN M 15 " pdb=" CG ASN M 15 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.90e+00 bond pdb=" CB ASN Y 15 " pdb=" CG ASN Y 15 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.83e+00 bond pdb=" CB ASN G 15 " pdb=" CG ASN G 15 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.78e+00 bond pdb=" CB ASN V 15 " pdb=" CG ASN V 15 " ideal model delta sigma weight residual 1.516 1.557 -0.041 2.50e-02 1.60e+03 2.74e+00 bond pdb=" CB ASN J 15 " pdb=" CG ASN J 15 " ideal model delta sigma weight residual 1.516 1.556 -0.040 2.50e-02 1.60e+03 2.54e+00 ... (remaining 17995 not shown) Histogram of bond angle deviations from ideal: 92.89 - 101.12: 87 101.12 - 109.35: 1686 109.35 - 117.58: 11968 117.58 - 125.81: 10460 125.81 - 134.04: 279 Bond angle restraints: 24480 Sorted by residual: angle pdb=" CA ASN J 15 " pdb=" CB ASN J 15 " pdb=" CG ASN J 15 " ideal model delta sigma weight residual 112.60 116.23 -3.63 1.00e+00 1.00e+00 1.32e+01 angle pdb=" CA ASN M 15 " pdb=" CB ASN M 15 " pdb=" CG ASN M 15 " ideal model delta sigma weight residual 112.60 116.22 -3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" CA ASN b 15 " pdb=" CB ASN b 15 " pdb=" CG ASN b 15 " ideal model delta sigma weight residual 112.60 116.22 -3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" CA LEU M 24 " pdb=" CB LEU M 24 " pdb=" CG LEU M 24 " ideal model delta sigma weight residual 116.30 128.86 -12.56 3.50e+00 8.16e-02 1.29e+01 angle pdb=" CA ASN G 15 " pdb=" CB ASN G 15 " pdb=" CG ASN G 15 " ideal model delta sigma weight residual 112.60 116.16 -3.56 1.00e+00 1.00e+00 1.27e+01 ... (remaining 24475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.62: 10972 25.62 - 51.25: 1181 51.25 - 76.87: 145 76.87 - 102.49: 12 102.49 - 128.11: 10 Dihedral angle restraints: 12320 sinusoidal: 6490 harmonic: 5830 Sorted by residual: dihedral pdb=" O21 3PE J 301 " pdb=" C2 3PE J 301 " pdb=" C3 3PE J 301 " pdb=" O31 3PE J 301 " ideal model delta sinusoidal sigma weight residual 60.47 -171.42 -128.11 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O21 3PE V 301 " pdb=" C2 3PE V 301 " pdb=" C3 3PE V 301 " pdb=" O31 3PE V 301 " ideal model delta sinusoidal sigma weight residual 60.47 -171.68 -127.85 1 3.00e+01 1.11e-03 1.72e+01 dihedral pdb=" O21 3PE Y 302 " pdb=" C2 3PE Y 302 " pdb=" C3 3PE Y 302 " pdb=" O31 3PE Y 302 " ideal model delta sinusoidal sigma weight residual 60.47 -172.47 -127.06 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 12317 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2065 0.041 - 0.082: 629 0.082 - 0.123: 150 0.123 - 0.164: 23 0.164 - 0.205: 13 Chirality restraints: 2880 Sorted by residual: chirality pdb=" CB THR A 29 " pdb=" CA THR A 29 " pdb=" OG1 THR A 29 " pdb=" CG2 THR A 29 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB THR b 29 " pdb=" CA THR b 29 " pdb=" OG1 THR b 29 " pdb=" CG2 THR b 29 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB THR S 29 " pdb=" CA THR S 29 " pdb=" OG1 THR S 29 " pdb=" CG2 THR S 29 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 2877 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN V 15 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ASN V 15 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN V 15 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS V 16 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN Y 15 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ASN Y 15 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN Y 15 " -0.023 2.00e-02 2.50e+03 pdb=" N CYS Y 16 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 15 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASN M 15 " -0.059 2.00e-02 2.50e+03 pdb=" O ASN M 15 " 0.023 2.00e-02 2.50e+03 pdb=" N CYS M 16 " 0.019 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 69 2.58 - 3.16: 12295 3.16 - 3.74: 24198 3.74 - 4.32: 33064 4.32 - 4.90: 57192 Nonbonded interactions: 126818 Sorted by model distance: nonbonded pdb=" O ASN b 15 " pdb=" ND2 ASN b 15 " model vdw 2.001 2.520 nonbonded pdb=" O ASN A 15 " pdb=" ND2 ASN A 15 " model vdw 2.017 2.520 nonbonded pdb=" O ASN S 15 " pdb=" ND2 ASN S 15 " model vdw 2.090 2.520 nonbonded pdb=" O ASN P 15 " pdb=" ND2 ASN P 15 " model vdw 2.195 2.520 nonbonded pdb=" O ASN B 15 " pdb=" ND2 ASN B 15 " model vdw 2.205 2.520 ... (remaining 126813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 229) selection = (chain 'B' and resid 3 through 229) selection = (chain 'G' and resid 3 through 229) selection = (chain 'J' and resid 3 through 229) selection = (chain 'M' and resid 3 through 229) selection = (chain 'P' and resid 3 through 229) selection = (chain 'S' and resid 3 through 229) selection = (chain 'V' and resid 3 through 229) selection = (chain 'Y' and resid 3 through 229) selection = (chain 'b' and resid 3 through 229) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.240 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: 0.010 Extract box with map and model: 12.750 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 43.950 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.120 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:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18000 Z= 0.170 Angle : 0.699 12.564 24480 Z= 0.376 Chirality : 0.042 0.205 2880 Planarity : 0.005 0.039 2770 Dihedral : 18.236 128.114 8470 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 8.33 % Allowed : 26.95 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.19), residues: 1990 helix: -0.36 (0.15), residues: 1340 sheet: -0.17 (0.50), residues: 110 loop : -1.47 (0.28), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 25 HIS 0.004 0.001 HIS M 146 PHE 0.009 0.001 PHE P 200 TYR 0.010 0.001 TYR B 143 ARG 0.005 0.000 ARG P 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 308 time to evaluate : 1.825 Fit side-chains REVERT: A 11 ILE cc_start: 0.7783 (mt) cc_final: 0.7578 (mt) REVERT: A 28 LEU cc_start: 0.7950 (mt) cc_final: 0.7579 (tp) REVERT: A 79 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8424 (tp) REVERT: B 28 LEU cc_start: 0.7944 (mt) cc_final: 0.7461 (tp) REVERT: B 47 ASP cc_start: 0.8904 (p0) cc_final: 0.8613 (p0) REVERT: G 28 LEU cc_start: 0.7950 (mt) cc_final: 0.7495 (tp) REVERT: J 28 LEU cc_start: 0.8026 (mt) cc_final: 0.7543 (tp) REVERT: M 28 LEU cc_start: 0.7952 (mt) cc_final: 0.7468 (tp) REVERT: P 28 LEU cc_start: 0.7926 (mt) cc_final: 0.7455 (tp) REVERT: P 47 ASP cc_start: 0.8881 (p0) cc_final: 0.8594 (p0) REVERT: S 28 LEU cc_start: 0.7900 (mt) cc_final: 0.7539 (tp) REVERT: V 28 LEU cc_start: 0.8029 (mt) cc_final: 0.7572 (tp) REVERT: Y 28 LEU cc_start: 0.7988 (mt) cc_final: 0.7527 (tp) REVERT: b 28 LEU cc_start: 0.7929 (mt) cc_final: 0.7539 (tp) REVERT: b 79 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8391 (tp) outliers start: 145 outliers final: 80 residues processed: 411 average time/residue: 0.9780 time to fit residues: 464.6132 Evaluate side-chains 311 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 229 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 74 HIS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 151 THR Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 176 THR Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 176 THR Chi-restraints excluded: chain M residue 189 SER Chi-restraints excluded: chain P residue 70 SER Chi-restraints excluded: chain P residue 74 HIS Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain P residue 176 THR Chi-restraints excluded: chain P residue 189 SER Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 74 HIS Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 176 THR Chi-restraints excluded: chain S residue 189 SER Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 72 VAL Chi-restraints excluded: chain V residue 74 HIS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 151 THR Chi-restraints excluded: chain V residue 176 THR Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 176 THR Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 74 HIS Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 151 THR Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 189 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 181 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 46 GLN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18000 Z= 0.195 Angle : 0.631 7.897 24480 Z= 0.293 Chirality : 0.042 0.158 2880 Planarity : 0.005 0.045 2770 Dihedral : 13.878 108.899 4994 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.23 % Allowed : 26.78 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.19), residues: 1990 helix: 0.05 (0.14), residues: 1360 sheet: 0.03 (0.52), residues: 110 loop : -1.76 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP S 25 HIS 0.008 0.003 HIS V 74 PHE 0.011 0.001 PHE P 52 TYR 0.008 0.001 TYR S 66 ARG 0.005 0.000 ARG P 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 248 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7358 (tp) REVERT: A 74 HIS cc_start: 0.6776 (OUTLIER) cc_final: 0.5692 (p90) REVERT: A 79 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 227 ARG cc_start: 0.4584 (OUTLIER) cc_final: 0.3829 (tpm-80) REVERT: B 28 LEU cc_start: 0.7870 (mt) cc_final: 0.7384 (tp) REVERT: B 47 ASP cc_start: 0.8956 (p0) cc_final: 0.8669 (p0) REVERT: B 227 ARG cc_start: 0.4831 (OUTLIER) cc_final: 0.4081 (tpm-80) REVERT: G 74 HIS cc_start: 0.6782 (OUTLIER) cc_final: 0.5851 (p90) REVERT: G 227 ARG cc_start: 0.4546 (OUTLIER) cc_final: 0.3818 (tpm-80) REVERT: J 28 LEU cc_start: 0.7641 (mt) cc_final: 0.7238 (tp) REVERT: J 74 HIS cc_start: 0.6958 (OUTLIER) cc_final: 0.5917 (p90) REVERT: M 28 LEU cc_start: 0.7782 (mt) cc_final: 0.7361 (tp) REVERT: M 74 HIS cc_start: 0.6777 (OUTLIER) cc_final: 0.5822 (p90) REVERT: P 28 LEU cc_start: 0.7615 (mt) cc_final: 0.7273 (tp) REVERT: P 47 ASP cc_start: 0.8935 (p0) cc_final: 0.8628 (p0) REVERT: S 28 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7358 (tp) REVERT: S 74 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.5869 (p90) REVERT: S 227 ARG cc_start: 0.4770 (OUTLIER) cc_final: 0.3858 (tpm-80) REVERT: V 28 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7316 (tp) REVERT: V 74 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.5956 (p90) REVERT: Y 28 LEU cc_start: 0.7792 (mt) cc_final: 0.7403 (tp) REVERT: Y 74 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.5850 (p90) REVERT: b 28 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7337 (tp) REVERT: b 74 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.5726 (p90) REVERT: b 79 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8472 (tp) outliers start: 91 outliers final: 54 residues processed: 314 average time/residue: 1.0895 time to fit residues: 389.8590 Evaluate side-chains 305 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 233 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 74 HIS Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 74 HIS Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 74 HIS Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 189 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 74 HIS Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 74 HIS Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain P residue 74 HIS Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 189 SER Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 74 HIS Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 189 SER Chi-restraints excluded: chain S residue 227 ARG Chi-restraints excluded: chain V residue 28 LEU Chi-restraints excluded: chain V residue 74 HIS Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain Y residue 7 LEU Chi-restraints excluded: chain Y residue 74 HIS Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 227 ARG Chi-restraints excluded: chain b residue 28 LEU Chi-restraints excluded: chain b residue 74 HIS Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 189 SER Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 181 optimal weight: 4.9990 chunk 196 optimal weight: 0.4980 chunk 162 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18000 Z= 0.231 Angle : 0.644 8.441 24480 Z= 0.301 Chirality : 0.044 0.155 2880 Planarity : 0.005 0.043 2770 Dihedral : 13.351 101.964 4957 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.92 % Allowed : 23.85 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1990 helix: 0.31 (0.14), residues: 1360 sheet: 0.00 (0.52), residues: 110 loop : -2.26 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP b 202 HIS 0.006 0.003 HIS V 74 PHE 0.011 0.001 PHE b 52 TYR 0.011 0.001 TYR P 162 ARG 0.004 0.000 ARG P 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 237 time to evaluate : 1.922 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7878 (mt) cc_final: 0.7462 (tp) REVERT: A 79 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8505 (tp) REVERT: A 227 ARG cc_start: 0.4676 (OUTLIER) cc_final: 0.3731 (tpm-80) REVERT: B 28 LEU cc_start: 0.7947 (mt) cc_final: 0.7448 (tp) REVERT: B 30 MET cc_start: 0.8604 (tpp) cc_final: 0.8398 (tpp) REVERT: B 47 ASP cc_start: 0.8897 (p0) cc_final: 0.8624 (p0) REVERT: B 227 ARG cc_start: 0.4736 (OUTLIER) cc_final: 0.4108 (tpm-80) REVERT: G 227 ARG cc_start: 0.4571 (OUTLIER) cc_final: 0.3817 (tpm-80) REVERT: J 28 LEU cc_start: 0.7892 (mt) cc_final: 0.7521 (tp) REVERT: J 213 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8423 (mp) REVERT: M 28 LEU cc_start: 0.7877 (mt) cc_final: 0.7553 (tp) REVERT: M 222 ARG cc_start: 0.7356 (OUTLIER) cc_final: 0.6655 (ttp80) REVERT: P 28 LEU cc_start: 0.7793 (mt) cc_final: 0.7440 (tp) REVERT: P 47 ASP cc_start: 0.8888 (p0) cc_final: 0.8620 (p0) REVERT: P 76 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8357 (mpp-170) REVERT: S 28 LEU cc_start: 0.7876 (mt) cc_final: 0.7424 (tp) REVERT: S 227 ARG cc_start: 0.4757 (OUTLIER) cc_final: 0.3873 (tpm-80) REVERT: V 28 LEU cc_start: 0.7812 (mt) cc_final: 0.7566 (tp) REVERT: V 213 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8432 (mp) REVERT: Y 28 LEU cc_start: 0.7899 (mt) cc_final: 0.7589 (tp) REVERT: Y 222 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6685 (ttp80) REVERT: b 28 LEU cc_start: 0.7866 (mt) cc_final: 0.7445 (tp) REVERT: b 79 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8501 (tp) outliers start: 103 outliers final: 57 residues processed: 316 average time/residue: 1.0966 time to fit residues: 391.5925 Evaluate side-chains 292 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 224 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 222 ARG Chi-restraints excluded: chain P residue 76 ARG Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 227 ARG Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 213 LEU Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain Y residue 222 ARG Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 193 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 46 GLN P 15 ASN S 15 ASN Y 15 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18000 Z= 0.301 Angle : 0.687 9.824 24480 Z= 0.320 Chirality : 0.046 0.152 2880 Planarity : 0.005 0.046 2770 Dihedral : 13.184 101.940 4929 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 5.52 % Allowed : 23.68 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 1990 helix: 0.33 (0.14), residues: 1380 sheet: 0.01 (0.53), residues: 110 loop : -2.33 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP M 202 HIS 0.007 0.003 HIS b 146 PHE 0.011 0.002 PHE P 52 TYR 0.013 0.002 TYR G 66 ARG 0.004 0.000 ARG P 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 227 time to evaluate : 1.864 Fit side-chains REVERT: A 28 LEU cc_start: 0.7875 (mt) cc_final: 0.7443 (tp) REVERT: A 79 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8454 (tp) REVERT: A 227 ARG cc_start: 0.4780 (OUTLIER) cc_final: 0.3795 (tpm-80) REVERT: B 28 LEU cc_start: 0.7938 (mt) cc_final: 0.7439 (tp) REVERT: B 47 ASP cc_start: 0.8886 (p0) cc_final: 0.8619 (p0) REVERT: B 213 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8587 (mt) REVERT: G 28 LEU cc_start: 0.8087 (mt) cc_final: 0.7576 (tp) REVERT: G 227 ARG cc_start: 0.4562 (OUTLIER) cc_final: 0.3851 (tpm-80) REVERT: J 24 LEU cc_start: 0.8272 (tp) cc_final: 0.7780 (mt) REVERT: J 28 LEU cc_start: 0.7881 (mt) cc_final: 0.7584 (tp) REVERT: J 221 ARG cc_start: 0.7709 (OUTLIER) cc_final: 0.7194 (ttp80) REVERT: J 222 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7015 (ttp80) REVERT: M 10 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8326 (mp) REVERT: M 24 LEU cc_start: 0.8270 (tp) cc_final: 0.7792 (mt) REVERT: M 28 LEU cc_start: 0.7940 (mt) cc_final: 0.7645 (tp) REVERT: M 74 HIS cc_start: 0.8038 (m90) cc_final: 0.7191 (t70) REVERT: M 222 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.6672 (ttp80) REVERT: P 28 LEU cc_start: 0.7858 (mt) cc_final: 0.7473 (tp) REVERT: P 47 ASP cc_start: 0.8877 (p0) cc_final: 0.8597 (p0) REVERT: S 28 LEU cc_start: 0.7880 (mt) cc_final: 0.7410 (tp) REVERT: V 24 LEU cc_start: 0.8273 (tp) cc_final: 0.7769 (mt) REVERT: V 28 LEU cc_start: 0.7874 (mt) cc_final: 0.7601 (tp) REVERT: V 213 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8499 (mt) REVERT: V 221 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7262 (ttp80) REVERT: V 222 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.6404 (ttp80) REVERT: Y 24 LEU cc_start: 0.8229 (tp) cc_final: 0.7740 (mt) REVERT: Y 28 LEU cc_start: 0.7995 (mt) cc_final: 0.7706 (tp) REVERT: Y 222 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.6704 (ttp80) REVERT: b 28 LEU cc_start: 0.7875 (mt) cc_final: 0.7444 (tp) REVERT: b 79 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8454 (tp) outliers start: 96 outliers final: 72 residues processed: 301 average time/residue: 1.0164 time to fit residues: 349.0277 Evaluate side-chains 307 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 222 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain M residue 222 ARG Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 102 THR Chi-restraints excluded: chain V residue 103 LEU Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 213 LEU Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain V residue 222 ARG Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain Y residue 222 ARG Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 79 LEU Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 173 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18000 Z= 0.240 Angle : 0.622 9.509 24480 Z= 0.289 Chirality : 0.044 0.157 2880 Planarity : 0.005 0.042 2770 Dihedral : 13.025 102.198 4926 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.69 % Allowed : 22.41 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.19), residues: 1990 helix: 0.58 (0.14), residues: 1380 sheet: 0.05 (0.53), residues: 110 loop : -2.39 (0.23), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP Y 202 HIS 0.006 0.002 HIS A 146 PHE 0.010 0.001 PHE P 52 TYR 0.012 0.002 TYR G 66 ARG 0.003 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 236 time to evaluate : 1.721 Fit side-chains REVERT: A 28 LEU cc_start: 0.7888 (mt) cc_final: 0.7506 (tp) REVERT: B 28 LEU cc_start: 0.7871 (mt) cc_final: 0.7440 (tp) REVERT: B 47 ASP cc_start: 0.8852 (p0) cc_final: 0.8594 (p0) REVERT: B 74 HIS cc_start: 0.8188 (m-70) cc_final: 0.7549 (m-70) REVERT: B 213 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8579 (mt) REVERT: G 28 LEU cc_start: 0.8061 (mt) cc_final: 0.7570 (tp) REVERT: J 24 LEU cc_start: 0.8240 (tp) cc_final: 0.7873 (mt) REVERT: J 28 LEU cc_start: 0.7776 (mt) cc_final: 0.7518 (tp) REVERT: J 213 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8490 (mt) REVERT: J 221 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7181 (ttp80) REVERT: M 10 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8248 (mp) REVERT: M 24 LEU cc_start: 0.8121 (tp) cc_final: 0.7802 (mt) REVERT: M 28 LEU cc_start: 0.7943 (mt) cc_final: 0.7661 (tp) REVERT: M 222 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6759 (ttp80) REVERT: P 28 LEU cc_start: 0.7729 (mt) cc_final: 0.7468 (tp) REVERT: P 47 ASP cc_start: 0.8824 (p0) cc_final: 0.8579 (p0) REVERT: S 28 LEU cc_start: 0.7905 (mt) cc_final: 0.7503 (tp) REVERT: V 24 LEU cc_start: 0.8204 (tp) cc_final: 0.7849 (mt) REVERT: V 28 LEU cc_start: 0.7805 (mt) cc_final: 0.7537 (tp) REVERT: V 213 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8497 (mt) REVERT: V 221 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7204 (ttp80) REVERT: Y 24 LEU cc_start: 0.8152 (tp) cc_final: 0.7812 (mt) REVERT: Y 28 LEU cc_start: 0.7966 (mt) cc_final: 0.7675 (tp) REVERT: b 28 LEU cc_start: 0.7886 (mt) cc_final: 0.7493 (tp) outliers start: 99 outliers final: 79 residues processed: 308 average time/residue: 0.9685 time to fit residues: 342.2597 Evaluate side-chains 310 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 224 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain M residue 10 LEU Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 83 VAL Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain M residue 222 ARG Chi-restraints excluded: chain P residue 70 SER Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 213 LEU Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 29 THR Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 83 VAL Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 83 VAL Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 113 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 18000 Z= 0.149 Angle : 0.535 8.873 24480 Z= 0.246 Chirality : 0.041 0.162 2880 Planarity : 0.004 0.038 2770 Dihedral : 12.685 102.118 4920 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.71 % Allowed : 23.56 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1990 helix: 0.97 (0.15), residues: 1380 sheet: 0.12 (0.52), residues: 110 loop : -2.29 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 202 HIS 0.004 0.002 HIS G 146 PHE 0.007 0.001 PHE S 9 TYR 0.008 0.001 TYR G 66 ARG 0.002 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 230 time to evaluate : 1.663 Fit side-chains REVERT: A 28 LEU cc_start: 0.7816 (mt) cc_final: 0.7457 (tp) REVERT: B 28 LEU cc_start: 0.7816 (mt) cc_final: 0.7464 (tp) REVERT: B 47 ASP cc_start: 0.8856 (p0) cc_final: 0.8618 (p0) REVERT: B 74 HIS cc_start: 0.8141 (m-70) cc_final: 0.7551 (m-70) REVERT: B 76 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8327 (mpp-170) REVERT: G 28 LEU cc_start: 0.8023 (mt) cc_final: 0.7543 (tp) REVERT: J 24 LEU cc_start: 0.8235 (tp) cc_final: 0.7904 (mt) REVERT: J 28 LEU cc_start: 0.7736 (mt) cc_final: 0.7515 (tp) REVERT: J 213 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8469 (mt) REVERT: J 221 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7125 (ttp80) REVERT: M 24 LEU cc_start: 0.8080 (tp) cc_final: 0.7822 (mt) REVERT: M 28 LEU cc_start: 0.7955 (mt) cc_final: 0.7702 (tp) REVERT: P 28 LEU cc_start: 0.7591 (mt) cc_final: 0.7341 (tp) REVERT: P 47 ASP cc_start: 0.8805 (p0) cc_final: 0.8550 (p0) REVERT: S 28 LEU cc_start: 0.7840 (mt) cc_final: 0.7432 (tp) REVERT: S 74 HIS cc_start: 0.8145 (m-70) cc_final: 0.7634 (m-70) REVERT: V 24 LEU cc_start: 0.8241 (tp) cc_final: 0.7909 (mt) REVERT: V 28 LEU cc_start: 0.7748 (mt) cc_final: 0.7538 (tp) REVERT: V 213 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8489 (mt) REVERT: V 221 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7144 (ttp80) REVERT: Y 24 LEU cc_start: 0.8044 (tp) cc_final: 0.7778 (mt) REVERT: Y 28 LEU cc_start: 0.7974 (mt) cc_final: 0.7729 (tp) REVERT: b 28 LEU cc_start: 0.7851 (mt) cc_final: 0.7456 (tp) REVERT: b 221 ARG cc_start: 0.7667 (ttm170) cc_final: 0.7457 (ttp-170) outliers start: 82 outliers final: 62 residues processed: 298 average time/residue: 1.0087 time to fit residues: 344.9317 Evaluate side-chains 292 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 225 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 94 VAL Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 6 LEU Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 94 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 213 LEU Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 94 VAL Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 94 VAL Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 218 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 141 optimal weight: 0.0000 chunk 109 optimal weight: 6.9990 chunk 162 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 15 ASN ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18000 Z= 0.133 Angle : 0.509 8.430 24480 Z= 0.233 Chirality : 0.040 0.162 2880 Planarity : 0.004 0.036 2770 Dihedral : 12.398 102.050 4920 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.56 % Allowed : 24.66 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1990 helix: 1.35 (0.15), residues: 1370 sheet: 0.26 (0.51), residues: 110 loop : -2.24 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 202 HIS 0.004 0.001 HIS S 146 PHE 0.006 0.001 PHE S 9 TYR 0.007 0.001 TYR J 66 ARG 0.002 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 233 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7946 (mt) cc_final: 0.7569 (tp) REVERT: A 76 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8139 (mpp-170) REVERT: B 28 LEU cc_start: 0.7833 (mt) cc_final: 0.7486 (tp) REVERT: B 47 ASP cc_start: 0.8817 (p0) cc_final: 0.8593 (p0) REVERT: B 74 HIS cc_start: 0.8082 (m-70) cc_final: 0.7538 (m-70) REVERT: B 76 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8368 (mpp-170) REVERT: B 176 THR cc_start: 0.8358 (p) cc_final: 0.7988 (t) REVERT: G 28 LEU cc_start: 0.7948 (mt) cc_final: 0.7473 (tp) REVERT: G 74 HIS cc_start: 0.8173 (m-70) cc_final: 0.7653 (m-70) REVERT: G 227 ARG cc_start: 0.4919 (OUTLIER) cc_final: 0.4041 (tpm-80) REVERT: J 24 LEU cc_start: 0.8229 (tp) cc_final: 0.7942 (mt) REVERT: J 28 LEU cc_start: 0.7738 (mt) cc_final: 0.7529 (tp) REVERT: J 221 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7062 (ttp80) REVERT: M 24 LEU cc_start: 0.8156 (tp) cc_final: 0.7884 (mt) REVERT: M 28 LEU cc_start: 0.7886 (mt) cc_final: 0.7685 (tp) REVERT: P 28 LEU cc_start: 0.7613 (mt) cc_final: 0.7377 (tp) REVERT: P 47 ASP cc_start: 0.8788 (p0) cc_final: 0.8557 (p0) REVERT: P 176 THR cc_start: 0.8450 (p) cc_final: 0.8052 (t) REVERT: S 28 LEU cc_start: 0.7782 (mt) cc_final: 0.7373 (tp) REVERT: S 74 HIS cc_start: 0.8063 (m-70) cc_final: 0.7674 (m-70) REVERT: V 24 LEU cc_start: 0.8188 (tp) cc_final: 0.7906 (mt) REVERT: V 213 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8526 (mt) REVERT: V 221 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7051 (ttp80) REVERT: Y 24 LEU cc_start: 0.8110 (tp) cc_final: 0.7847 (mt) REVERT: Y 28 LEU cc_start: 0.7919 (mt) cc_final: 0.7718 (tp) REVERT: b 28 LEU cc_start: 0.7847 (mt) cc_final: 0.7463 (tp) REVERT: b 76 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8134 (mpp-170) REVERT: b 221 ARG cc_start: 0.7607 (ttm170) cc_final: 0.7392 (ttp-170) outliers start: 62 outliers final: 47 residues processed: 291 average time/residue: 1.0090 time to fit residues: 334.9885 Evaluate side-chains 278 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 224 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 94 VAL Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 103 LEU Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 213 LEU Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Chi-restraints excluded: chain b residue 227 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 0.0570 chunk 115 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.8108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 18000 Z= 0.151 Angle : 0.525 8.834 24480 Z= 0.240 Chirality : 0.041 0.160 2880 Planarity : 0.004 0.038 2770 Dihedral : 12.219 101.742 4913 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.14 % Allowed : 23.97 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 1990 helix: 1.47 (0.15), residues: 1360 sheet: 0.36 (0.52), residues: 110 loop : -2.17 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 202 HIS 0.005 0.002 HIS b 146 PHE 0.006 0.001 PHE S 9 TYR 0.009 0.001 TYR J 66 ARG 0.002 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 228 time to evaluate : 1.851 Fit side-chains REVERT: A 28 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7597 (tp) REVERT: A 76 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8168 (mpp-170) REVERT: A 102 THR cc_start: 0.7663 (t) cc_final: 0.7070 (p) REVERT: B 28 LEU cc_start: 0.7832 (mt) cc_final: 0.7485 (tp) REVERT: B 47 ASP cc_start: 0.8813 (p0) cc_final: 0.8572 (p0) REVERT: B 74 HIS cc_start: 0.8082 (m-70) cc_final: 0.7560 (m-70) REVERT: B 76 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8368 (mpp-170) REVERT: B 227 ARG cc_start: 0.4738 (OUTLIER) cc_final: 0.3989 (tpm-80) REVERT: G 28 LEU cc_start: 0.8022 (mt) cc_final: 0.7553 (tp) REVERT: G 74 HIS cc_start: 0.8186 (m-70) cc_final: 0.7675 (m-70) REVERT: G 227 ARG cc_start: 0.4890 (OUTLIER) cc_final: 0.4037 (tpm-80) REVERT: J 24 LEU cc_start: 0.8254 (tp) cc_final: 0.7963 (mt) REVERT: J 28 LEU cc_start: 0.7748 (mt) cc_final: 0.7524 (tp) REVERT: J 221 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7026 (ttp80) REVERT: M 24 LEU cc_start: 0.8087 (tp) cc_final: 0.7874 (mt) REVERT: M 28 LEU cc_start: 0.7892 (mt) cc_final: 0.7691 (tp) REVERT: P 28 LEU cc_start: 0.7629 (mt) cc_final: 0.7369 (tp) REVERT: P 47 ASP cc_start: 0.8784 (p0) cc_final: 0.8555 (p0) REVERT: S 28 LEU cc_start: 0.7786 (mt) cc_final: 0.7381 (tp) REVERT: S 74 HIS cc_start: 0.8145 (m-70) cc_final: 0.7675 (m-70) REVERT: S 198 MET cc_start: 0.8768 (mtt) cc_final: 0.8558 (mtt) REVERT: V 24 LEU cc_start: 0.8189 (tp) cc_final: 0.7907 (mt) REVERT: V 221 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7029 (ttp80) REVERT: Y 24 LEU cc_start: 0.8061 (tp) cc_final: 0.7829 (mt) REVERT: Y 28 LEU cc_start: 0.7946 (mt) cc_final: 0.7737 (tp) REVERT: b 28 LEU cc_start: 0.7882 (mt) cc_final: 0.7515 (tp) REVERT: b 76 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8170 (mpp-170) REVERT: b 221 ARG cc_start: 0.7589 (ttm170) cc_final: 0.7371 (ttp-170) outliers start: 72 outliers final: 59 residues processed: 288 average time/residue: 1.0770 time to fit residues: 352.1638 Evaluate side-chains 291 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 224 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 70 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 2.9990 chunk 168 optimal weight: 0.5980 chunk 179 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18000 Z= 0.182 Angle : 0.556 9.271 24480 Z= 0.256 Chirality : 0.042 0.157 2880 Planarity : 0.004 0.039 2770 Dihedral : 12.150 101.474 4912 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.91 % Allowed : 24.20 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1990 helix: 1.50 (0.14), residues: 1360 sheet: 0.37 (0.52), residues: 110 loop : -2.23 (0.23), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 202 HIS 0.005 0.002 HIS M 146 PHE 0.008 0.001 PHE P 52 TYR 0.010 0.001 TYR J 66 ARG 0.002 0.000 ARG Y 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 229 time to evaluate : 1.851 Fit side-chains REVERT: A 28 LEU cc_start: 0.7987 (mt) cc_final: 0.7567 (tp) REVERT: A 76 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8183 (mpp-170) REVERT: A 102 THR cc_start: 0.7621 (t) cc_final: 0.7057 (p) REVERT: B 28 LEU cc_start: 0.7879 (mt) cc_final: 0.7517 (tp) REVERT: B 47 ASP cc_start: 0.8833 (p0) cc_final: 0.8590 (p0) REVERT: B 74 HIS cc_start: 0.8109 (m-70) cc_final: 0.7558 (m-70) REVERT: B 76 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8366 (mpp-170) REVERT: G 28 LEU cc_start: 0.8024 (mt) cc_final: 0.7559 (tp) REVERT: J 24 LEU cc_start: 0.8272 (tp) cc_final: 0.7969 (mt) REVERT: J 28 LEU cc_start: 0.7793 (mt) cc_final: 0.7548 (tp) REVERT: J 221 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7004 (ttp80) REVERT: M 24 LEU cc_start: 0.8078 (tp) cc_final: 0.7847 (mt) REVERT: M 28 LEU cc_start: 0.7937 (mt) cc_final: 0.7715 (tp) REVERT: P 28 LEU cc_start: 0.7789 (mt) cc_final: 0.7582 (tp) REVERT: P 47 ASP cc_start: 0.8802 (p0) cc_final: 0.8539 (p0) REVERT: S 28 LEU cc_start: 0.7781 (mt) cc_final: 0.7349 (tp) REVERT: S 74 HIS cc_start: 0.8216 (m-70) cc_final: 0.7717 (m-70) REVERT: V 24 LEU cc_start: 0.8242 (tp) cc_final: 0.7949 (mt) REVERT: V 221 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7028 (ttp80) REVERT: Y 28 LEU cc_start: 0.8000 (mt) cc_final: 0.7766 (tp) REVERT: b 28 LEU cc_start: 0.8002 (mt) cc_final: 0.7618 (tp) REVERT: b 76 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8184 (mpp-170) REVERT: b 221 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7364 (ttp-170) outliers start: 68 outliers final: 60 residues processed: 286 average time/residue: 1.0153 time to fit residues: 331.5903 Evaluate side-chains 289 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 224 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 70 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 83 VAL Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 199 optimal weight: 3.9990 chunk 183 optimal weight: 0.4980 chunk 158 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18000 Z= 0.152 Angle : 0.521 8.863 24480 Z= 0.239 Chirality : 0.041 0.159 2880 Planarity : 0.004 0.037 2770 Dihedral : 12.021 101.123 4912 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.97 % Allowed : 24.37 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 1990 helix: 1.67 (0.15), residues: 1360 sheet: 0.41 (0.52), residues: 110 loop : -2.19 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Y 202 HIS 0.004 0.002 HIS G 146 PHE 0.007 0.001 PHE G 9 TYR 0.009 0.001 TYR J 66 ARG 0.002 0.000 ARG Y 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3980 Ramachandran restraints generated. 1990 Oldfield, 0 Emsley, 1990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 228 time to evaluate : 1.927 Fit side-chains REVERT: A 28 LEU cc_start: 0.7971 (mt) cc_final: 0.7594 (tp) REVERT: A 76 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8168 (mpp-170) REVERT: A 102 THR cc_start: 0.7653 (t) cc_final: 0.7106 (p) REVERT: B 28 LEU cc_start: 0.7873 (mt) cc_final: 0.7508 (tp) REVERT: B 47 ASP cc_start: 0.8806 (p0) cc_final: 0.8576 (p0) REVERT: B 74 HIS cc_start: 0.8079 (m-70) cc_final: 0.7561 (m-70) REVERT: B 76 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8379 (mpp-170) REVERT: G 28 LEU cc_start: 0.7962 (mt) cc_final: 0.7487 (tp) REVERT: G 74 HIS cc_start: 0.8187 (m-70) cc_final: 0.7685 (m-70) REVERT: J 24 LEU cc_start: 0.8201 (tp) cc_final: 0.7965 (mt) REVERT: J 28 LEU cc_start: 0.7739 (mt) cc_final: 0.7513 (tp) REVERT: J 221 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7297 (ttp-170) REVERT: M 24 LEU cc_start: 0.8115 (tp) cc_final: 0.7877 (mt) REVERT: M 28 LEU cc_start: 0.7931 (mt) cc_final: 0.7719 (tp) REVERT: P 28 LEU cc_start: 0.7734 (mt) cc_final: 0.7494 (tp) REVERT: P 47 ASP cc_start: 0.8786 (p0) cc_final: 0.8533 (p0) REVERT: S 28 LEU cc_start: 0.7740 (mt) cc_final: 0.7320 (tp) REVERT: S 74 HIS cc_start: 0.8098 (m-70) cc_final: 0.7711 (m-70) REVERT: V 24 LEU cc_start: 0.8170 (tp) cc_final: 0.7947 (mt) REVERT: V 221 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7018 (ttp80) REVERT: Y 28 LEU cc_start: 0.7961 (mt) cc_final: 0.7750 (tp) REVERT: Y 102 THR cc_start: 0.7413 (t) cc_final: 0.6802 (p) REVERT: b 28 LEU cc_start: 0.7878 (mt) cc_final: 0.7572 (tp) REVERT: b 76 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8170 (mpp-170) REVERT: b 102 THR cc_start: 0.7560 (t) cc_final: 0.6965 (p) REVERT: b 221 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7366 (ttp-170) outliers start: 69 outliers final: 61 residues processed: 286 average time/residue: 1.0684 time to fit residues: 347.7185 Evaluate side-chains 290 residues out of total 1740 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 224 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 138 ASP Chi-restraints excluded: chain B residue 146 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 70 SER Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 146 HIS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 208 SER Chi-restraints excluded: chain G residue 218 CYS Chi-restraints excluded: chain J residue 7 LEU Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 146 HIS Chi-restraints excluded: chain J residue 148 LEU Chi-restraints excluded: chain J residue 181 THR Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 221 ARG Chi-restraints excluded: chain J residue 224 MET Chi-restraints excluded: chain M residue 70 SER Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 80 ILE Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 205 SER Chi-restraints excluded: chain M residue 208 SER Chi-restraints excluded: chain P residue 70 SER Chi-restraints excluded: chain P residue 146 HIS Chi-restraints excluded: chain P residue 148 LEU Chi-restraints excluded: chain P residue 208 SER Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 70 SER Chi-restraints excluded: chain S residue 146 HIS Chi-restraints excluded: chain S residue 148 LEU Chi-restraints excluded: chain S residue 181 THR Chi-restraints excluded: chain S residue 208 SER Chi-restraints excluded: chain V residue 70 SER Chi-restraints excluded: chain V residue 146 HIS Chi-restraints excluded: chain V residue 148 LEU Chi-restraints excluded: chain V residue 181 THR Chi-restraints excluded: chain V residue 208 SER Chi-restraints excluded: chain V residue 221 ARG Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 76 ARG Chi-restraints excluded: chain Y residue 80 ILE Chi-restraints excluded: chain Y residue 146 HIS Chi-restraints excluded: chain Y residue 181 THR Chi-restraints excluded: chain Y residue 205 SER Chi-restraints excluded: chain Y residue 208 SER Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain b residue 70 SER Chi-restraints excluded: chain b residue 76 ARG Chi-restraints excluded: chain b residue 80 ILE Chi-restraints excluded: chain b residue 146 HIS Chi-restraints excluded: chain b residue 205 SER Chi-restraints excluded: chain b residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.2980 chunk 158 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.106982 restraints weight = 17407.968| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.00 r_work: 0.2826 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18000 Z= 0.135 Angle : 0.511 8.761 24480 Z= 0.233 Chirality : 0.040 0.162 2880 Planarity : 0.004 0.036 2770 Dihedral : 11.948 101.102 4912 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.56 % Allowed : 24.71 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1990 helix: 1.77 (0.15), residues: 1360 sheet: 0.39 (0.51), residues: 110 loop : -2.15 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 202 HIS 0.004 0.001 HIS G 146 PHE 0.006 0.001 PHE G 9 TYR 0.008 0.001 TYR J 66 ARG 0.002 0.000 ARG Y 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5992.05 seconds wall clock time: 106 minutes 14.61 seconds (6374.61 seconds total)