Starting phenix.real_space_refine on Thu Mar 14 23:31:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwl_26835/03_2024/7uwl_26835.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwl_26835/03_2024/7uwl_26835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwl_26835/03_2024/7uwl_26835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwl_26835/03_2024/7uwl_26835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwl_26835/03_2024/7uwl_26835.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwl_26835/03_2024/7uwl_26835.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 6326 2.51 5 N 1792 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 93": "OE1" <-> "OE2" Residue "D GLU 51": "OE1" <-> "OE2" Residue "D GLU 129": "OE1" <-> "OE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10100 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 88} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1931 Classifications: {'peptide': 250} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 232} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1947 Classifications: {'peptide': 252} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 234} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2180 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 252} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2186 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 252} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.82, per 1000 atoms: 0.58 Number of scatterers: 10100 At special positions: 0 Unit cell: (201.948, 95.4352, 100.548, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 1902 8.00 N 1792 7.00 C 6326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 99 " distance=2.05 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 102 " distance=2.04 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 99 " distance=2.05 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 187 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 261 " distance=2.06 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 245 " - pdb=" SG CYS E 276 " distance=2.03 Simple disulfide: pdb=" SG CYS E 290 " - pdb=" SG CYS E 294 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 245 " - pdb=" SG CYS F 276 " distance=2.03 Simple disulfide: pdb=" SG CYS F 290 " - pdb=" SG CYS F 294 " 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 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 301 " - " ASN A 136 " " NAG B 301 " - " ASN B 136 " " NAG C 401 " - " ASN C 156 " " NAG C 402 " - " ASN C 67 " " NAG C 403 " - " ASN C 103 " " NAG D 401 " - " ASN D 103 " " NAG D 402 " - " ASN D 156 " " NAG D 403 " - " ASN D 67 " " NAG E 401 " - " ASN E 225 " " NAG E 402 " - " ASN E 265 " " NAG E 403 " - " ASN E 67 " " NAG F 401 " - " ASN F 67 " " NAG F 402 " - " ASN F 225 " " NAG F 403 " - " ASN F 265 " " NAG G 1 " - " ASN C 197 " " NAG H 1 " - " ASN C 183 " " NAG I 1 " - " ASN D 197 " " NAG J 1 " - " ASN D 183 " Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.6 seconds 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2360 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 25 sheets defined 7.5% alpha, 32.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 81 through 85 removed outlier: 3.510A pdb=" N SER A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'C' and resid 31 through 36 removed outlier: 4.327A pdb=" N MET C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 36' Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 254 through 258 removed outlier: 3.543A pdb=" N CYS C 257 " --> pdb=" O PHE C 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 36 removed outlier: 4.305A pdb=" N MET D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 36' Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.822A pdb=" N LYS D 168 " --> pdb=" O HIS D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 176 removed outlier: 3.748A pdb=" N LYS D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA D 176 " --> pdb=" O LYS D 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 109 removed outlier: 3.525A pdb=" N LEU E 109 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 192 removed outlier: 3.725A pdb=" N VAL E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.590A pdb=" N ILE F 106 " --> pdb=" O ASP F 103 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU F 109 " --> pdb=" O ILE F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 192 removed outlier: 4.206A pdb=" N VAL F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 198 Processing helix chain 'F' and resid 256 through 260 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96 Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.790A pdb=" N CYS A 115 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 143 removed outlier: 3.615A pdb=" N VAL A 164 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.462A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS D 264 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE D 211 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE D 217 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.462A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.757A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE D 184 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N VAL D 269 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA D 186 " --> pdb=" O VAL D 269 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.631A pdb=" N ARG B 91 " --> pdb=" O ARG B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'B' and resid 129 through 141 removed outlier: 4.151A pdb=" N ALA B 167 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N HIS B 135 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 165 " --> pdb=" O HIS B 135 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLN B 137 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG B 163 " --> pdb=" O GLN B 137 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 139 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU B 161 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N TYR B 141 " --> pdb=" O ARG B 159 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG B 159 " --> pdb=" O TYR B 141 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.690A pdb=" N LYS C 265 " --> pdb=" O MET B 176 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 207 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA C 209 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER C 220 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE C 211 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 218 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 175 through 176 removed outlier: 3.690A pdb=" N LYS C 265 " --> pdb=" O MET B 176 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE C 184 " --> pdb=" O LYS C 265 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N THR C 267 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA C 186 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 22 through 24 removed outlier: 3.520A pdb=" N GLN C 23 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER C 98 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL C 88 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL C 100 " --> pdb=" O ILE C 86 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C 86 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA C 83 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA C 138 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C 153 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.951A pdb=" N THR C 55 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER C 63 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 68 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 123 " --> pdb=" O VAL C 68 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.864A pdb=" N SER D 98 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N VAL D 88 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS D 102 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL D 133 " --> pdb=" O LYS D 91 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 138 " --> pdb=" O MET D 153 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 153 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 47 through 54 removed outlier: 3.677A pdb=" N GLY D 125 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL D 68 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D 123 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP D 70 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 206 through 207 removed outlier: 3.641A pdb=" N TYR D 207 " --> pdb=" O VAL D 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 74 through 83 removed outlier: 5.245A pdb=" N ASP E 75 " --> pdb=" O THR E 99 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 125 through 128 removed outlier: 3.821A pdb=" N VAL E 159 " --> pdb=" O LYS E 178 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS E 178 " --> pdb=" O VAL E 159 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E 176 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 208 through 210 removed outlier: 3.694A pdb=" N ARG E 218 " --> pdb=" O GLU E 210 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 246 through 252 removed outlier: 3.768A pdb=" N PHE E 246 " --> pdb=" O SER E 236 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 74 through 83 removed outlier: 5.117A pdb=" N ASP F 75 " --> pdb=" O THR F 99 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 124 through 128 removed outlier: 3.684A pdb=" N GLY F 111 " --> pdb=" O LEU F 164 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL F 159 " --> pdb=" O LYS F 178 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN F 176 " --> pdb=" O VAL F 161 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 208 through 210 Processing sheet with id=AC7, first strand: chain 'F' and resid 246 through 252 removed outlier: 3.734A pdb=" N PHE F 246 " --> pdb=" O SER F 236 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN F 231 " --> pdb=" O GLN F 284 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN F 284 " --> pdb=" O GLN F 231 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 627 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: 2.73 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1601 1.32 - 1.44: 2926 1.44 - 1.57: 5727 1.57 - 1.70: 0 1.70 - 1.83: 104 Bond restraints: 10358 Sorted by residual: bond pdb=" CD GLN E 231 " pdb=" NE2 GLN E 231 " ideal model delta sigma weight residual 1.328 1.230 0.098 2.10e-02 2.27e+03 2.16e+01 bond pdb=" C1 NAG F 402 " pdb=" O5 NAG F 402 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C1 NAG E 401 " pdb=" O5 NAG E 401 " ideal model delta sigma weight residual 1.406 1.479 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N THR F 69 " pdb=" CA THR F 69 " ideal model delta sigma weight residual 1.455 1.500 -0.045 1.60e-02 3.91e+03 7.79e+00 bond pdb=" N CYS D 102 " pdb=" CA CYS D 102 " ideal model delta sigma weight residual 1.455 1.489 -0.033 1.23e-02 6.61e+03 7.39e+00 ... (remaining 10353 not shown) Histogram of bond angle deviations from ideal: 95.69 - 103.37: 138 103.37 - 111.06: 4332 111.06 - 118.74: 4126 118.74 - 126.43: 5279 126.43 - 134.11: 218 Bond angle restraints: 14093 Sorted by residual: angle pdb=" C SER C 98 " pdb=" N CYS C 99 " pdb=" CA CYS C 99 " ideal model delta sigma weight residual 121.87 115.24 6.63 1.64e+00 3.72e-01 1.64e+01 angle pdb=" C LEU F 212 " pdb=" CA LEU F 212 " pdb=" CB LEU F 212 " ideal model delta sigma weight residual 116.34 110.90 5.44 1.40e+00 5.10e-01 1.51e+01 angle pdb=" C CYS D 102 " pdb=" CA CYS D 102 " pdb=" CB CYS D 102 " ideal model delta sigma weight residual 109.37 102.55 6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" CA CYS C 102 " pdb=" C CYS C 102 " pdb=" O CYS C 102 " ideal model delta sigma weight residual 121.11 117.38 3.73 1.13e+00 7.83e-01 1.09e+01 angle pdb=" N CYS C 99 " pdb=" CA CYS C 99 " pdb=" C CYS C 99 " ideal model delta sigma weight residual 108.96 113.67 -4.71 1.49e+00 4.50e-01 9.99e+00 ... (remaining 14088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.62: 5959 23.62 - 47.24: 528 47.24 - 70.87: 81 70.87 - 94.49: 9 94.49 - 118.11: 6 Dihedral angle restraints: 6583 sinusoidal: 2965 harmonic: 3618 Sorted by residual: dihedral pdb=" CB CYS C 162 " pdb=" SG CYS C 162 " pdb=" SG CYS C 173 " pdb=" CB CYS C 173 " ideal model delta sinusoidal sigma weight residual -86.00 -176.12 90.12 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" CB CYS D 87 " pdb=" SG CYS D 87 " pdb=" SG CYS D 99 " pdb=" CB CYS D 99 " ideal model delta sinusoidal sigma weight residual 93.00 14.71 78.29 1 1.00e+01 1.00e-02 7.65e+01 dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 99 " pdb=" CB CYS C 99 " ideal model delta sinusoidal sigma weight residual 93.00 38.21 54.79 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 6580 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1223 0.048 - 0.097: 291 0.097 - 0.145: 99 0.145 - 0.193: 10 0.193 - 0.241: 8 Chirality restraints: 1631 Sorted by residual: chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.24e+00 chirality pdb=" CA CYS D 102 " pdb=" N CYS D 102 " pdb=" C CYS D 102 " pdb=" CB CYS D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA CYS D 87 " pdb=" N CYS D 87 " pdb=" C CYS D 87 " pdb=" CB CYS D 87 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1628 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN E 231 " 0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" CD GLN E 231 " -0.063 2.00e-02 2.50e+03 pdb=" OE1 GLN E 231 " 0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN E 231 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.023 2.00e-02 2.50e+03 2.82e-02 9.95e+00 pdb=" CG ASN C 156 " 0.055 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " -0.004 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 156 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" CG ASN C 156 " 0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN C 156 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 156 " -0.017 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 296 2.69 - 3.24: 9298 3.24 - 3.79: 14646 3.79 - 4.35: 18403 4.35 - 4.90: 30313 Nonbonded interactions: 72956 Sorted by model distance: nonbonded pdb=" OG1 THR F 85 " pdb=" O ASP F 89 " model vdw 2.137 2.440 nonbonded pdb=" OD1 ASP F 89 " pdb=" OG1 THR F 194 " model vdw 2.164 2.440 nonbonded pdb=" OD1 ASP A 97 " pdb=" N LEU A 98 " model vdw 2.166 2.520 nonbonded pdb=" NE2 GLN E 231 " pdb=" OE1 GLN E 284 " model vdw 2.169 2.520 nonbonded pdb=" O SER B 88 " pdb=" OG SER B 88 " model vdw 2.217 2.440 ... (remaining 72951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 19 through 272 or resid 401 through 403)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 33 through 123 or (resid 124 and (name N or name CA or nam \ e C or name O or name CB )) or resid 125 through 303 or resid 401 through 403)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 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: 11.520 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 29.610 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 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 : 0.005 0.098 10358 Z= 0.314 Angle : 0.780 9.792 14093 Z= 0.396 Chirality : 0.049 0.241 1631 Planarity : 0.005 0.042 1800 Dihedral : 16.739 118.111 4145 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.63 % Allowed : 23.99 % Favored : 75.38 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 7.14 % 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: -1.39 (0.23), residues: 1216 helix: -1.68 (0.99), residues: 26 sheet: -0.13 (0.24), residues: 487 loop : -1.52 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 70 HIS 0.021 0.001 HIS E 139 PHE 0.010 0.001 PHE F 180 TYR 0.027 0.003 TYR C 253 ARG 0.019 0.001 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 276 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.7193 (p-80) cc_final: 0.6918 (p-80) REVERT: D 265 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7853 (mtmt) REVERT: F 142 TRP cc_start: 0.7501 (m100) cc_final: 0.6586 (m100) REVERT: F 154 ASP cc_start: 0.7543 (t0) cc_final: 0.7318 (m-30) outliers start: 7 outliers final: 4 residues processed: 279 average time/residue: 0.2641 time to fit residues: 97.3582 Evaluate side-chains 271 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 267 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 212 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.6980 chunk 92 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.0050 chunk 71 optimal weight: 1.9990 chunk 110 optimal weight: 8.9990 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN D 93 ASN D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10358 Z= 0.197 Angle : 0.702 10.097 14093 Z= 0.342 Chirality : 0.046 0.267 1631 Planarity : 0.005 0.041 1800 Dihedral : 10.594 95.929 1807 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.70 % Allowed : 22.09 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.30 (0.23), residues: 1216 helix: -1.52 (1.01), residues: 26 sheet: -0.03 (0.23), residues: 527 loop : -1.58 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 70 HIS 0.006 0.001 HIS E 148 PHE 0.011 0.001 PHE E 149 TYR 0.014 0.002 TYR F 157 ARG 0.007 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 268 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6344 (p-80) REVERT: B 124 MET cc_start: 0.5353 (ppp) cc_final: 0.5124 (ppp) REVERT: C 155 VAL cc_start: 0.6943 (OUTLIER) cc_final: 0.6633 (m) REVERT: C 230 GLN cc_start: 0.5955 (OUTLIER) cc_final: 0.5560 (tm-30) REVERT: D 193 THR cc_start: 0.8347 (m) cc_final: 0.7779 (p) REVERT: D 265 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7607 (mtmt) REVERT: F 79 GLN cc_start: 0.6695 (mm-40) cc_final: 0.6316 (tm-30) REVERT: F 80 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7460 (mt) REVERT: F 142 TRP cc_start: 0.7507 (m100) cc_final: 0.6577 (m100) REVERT: F 212 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.5688 (tt) outliers start: 41 outliers final: 23 residues processed: 289 average time/residue: 0.2590 time to fit residues: 98.1775 Evaluate side-chains 287 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 259 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 73 ARG Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 262 ILE Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 97 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 212 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 98 optimal weight: 0.0020 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 ASN D 131 ASN D 212 GLN E 79 GLN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10358 Z= 0.343 Angle : 0.782 11.082 14093 Z= 0.390 Chirality : 0.049 0.261 1631 Planarity : 0.006 0.055 1800 Dihedral : 10.672 90.955 1806 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 6.58 % Allowed : 22.00 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.66 (0.23), residues: 1216 helix: -1.59 (0.92), residues: 26 sheet: -0.37 (0.23), residues: 533 loop : -1.74 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 70 HIS 0.011 0.001 HIS E 148 PHE 0.014 0.002 PHE E 149 TYR 0.027 0.003 TYR A 141 ARG 0.006 0.001 ARG F 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 272 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6387 (OUTLIER) cc_final: 0.6072 (p-80) REVERT: A 166 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.6520 (mp) REVERT: B 124 MET cc_start: 0.5652 (ppp) cc_final: 0.5160 (ppp) REVERT: C 95 GLN cc_start: 0.7150 (mm-40) cc_final: 0.6928 (mm110) REVERT: C 155 VAL cc_start: 0.6993 (OUTLIER) cc_final: 0.6625 (m) REVERT: C 230 GLN cc_start: 0.5925 (OUTLIER) cc_final: 0.5528 (tm-30) REVERT: C 265 LYS cc_start: 0.8156 (tmtt) cc_final: 0.7856 (tmtt) REVERT: D 100 VAL cc_start: 0.7642 (m) cc_final: 0.7399 (p) REVERT: D 250 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7574 (mm) REVERT: F 129 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: F 142 TRP cc_start: 0.7605 (m100) cc_final: 0.6613 (m100) REVERT: F 143 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.6791 (mpt180) REVERT: F 186 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: F 212 LEU cc_start: 0.6081 (OUTLIER) cc_final: 0.5828 (tt) outliers start: 73 outliers final: 44 residues processed: 304 average time/residue: 0.2666 time to fit residues: 107.4955 Evaluate side-chains 320 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 267 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 105 THR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 287 PHE Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 58 optimal weight: 0.0050 chunk 105 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 98 optimal weight: 0.0010 overall best weight: 0.2678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10358 Z= 0.187 Angle : 0.714 10.147 14093 Z= 0.342 Chirality : 0.046 0.282 1631 Planarity : 0.004 0.038 1800 Dihedral : 9.923 87.311 1802 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.78 % Allowed : 24.26 % Favored : 70.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.55 (0.23), residues: 1216 helix: -1.51 (0.99), residues: 26 sheet: -0.34 (0.23), residues: 528 loop : -1.60 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 70 HIS 0.011 0.001 HIS E 148 PHE 0.011 0.001 PHE C 198 TYR 0.016 0.001 TYR D 253 ARG 0.005 0.000 ARG F 34 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 262 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.8253 (mt) cc_final: 0.8005 (mt) REVERT: A 135 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.5975 (p-80) REVERT: A 163 ARG cc_start: 0.7548 (tpp80) cc_final: 0.7046 (ttt90) REVERT: A 166 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6399 (mp) REVERT: B 124 MET cc_start: 0.5715 (ppp) cc_final: 0.5219 (ppp) REVERT: C 44 ASP cc_start: 0.6824 (m-30) cc_final: 0.6293 (m-30) REVERT: C 167 MET cc_start: 0.6086 (mmm) cc_final: 0.5815 (mmm) REVERT: C 230 GLN cc_start: 0.5910 (OUTLIER) cc_final: 0.5516 (tm-30) REVERT: C 265 LYS cc_start: 0.8038 (tmtt) cc_final: 0.7690 (tmtt) REVERT: D 250 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7660 (mm) REVERT: F 142 TRP cc_start: 0.7525 (m100) cc_final: 0.6526 (m100) REVERT: F 143 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6715 (mpt180) REVERT: F 217 LEU cc_start: -0.5149 (OUTLIER) cc_final: -0.6219 (tp) outliers start: 53 outliers final: 36 residues processed: 290 average time/residue: 0.2637 time to fit residues: 100.2143 Evaluate side-chains 303 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 261 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 66 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 281 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN E 120 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10358 Z= 0.335 Angle : 0.783 12.353 14093 Z= 0.383 Chirality : 0.048 0.265 1631 Planarity : 0.005 0.057 1800 Dihedral : 10.091 83.749 1800 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Rotamer: Outliers : 6.49 % Allowed : 23.35 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.67 (0.23), residues: 1216 helix: -1.47 (0.97), residues: 26 sheet: -0.40 (0.23), residues: 531 loop : -1.71 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 70 HIS 0.027 0.002 HIS F 163 PHE 0.013 0.002 PHE C 94 TYR 0.023 0.003 TYR A 141 ARG 0.004 0.001 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 273 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6309 (OUTLIER) cc_final: 0.6065 (p-80) REVERT: A 163 ARG cc_start: 0.7656 (tpp80) cc_final: 0.7123 (ttt90) REVERT: A 166 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6545 (mp) REVERT: B 124 MET cc_start: 0.5860 (ppp) cc_final: 0.5273 (ppp) REVERT: C 95 GLN cc_start: 0.7136 (mm-40) cc_final: 0.6872 (mm-40) REVERT: C 101 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6545 (ttt90) REVERT: C 230 GLN cc_start: 0.5832 (OUTLIER) cc_final: 0.5437 (tm-30) REVERT: C 265 LYS cc_start: 0.8146 (tmtt) cc_final: 0.7753 (tmtt) REVERT: D 100 VAL cc_start: 0.7692 (m) cc_final: 0.7405 (p) REVERT: D 250 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7684 (mm) REVERT: F 143 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.6772 (mpt180) REVERT: F 156 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7445 (mm-30) REVERT: F 212 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5672 (tt) REVERT: F 217 LEU cc_start: -0.5055 (OUTLIER) cc_final: -0.6103 (tp) REVERT: F 270 LEU cc_start: -0.5793 (OUTLIER) cc_final: -0.6091 (mp) outliers start: 72 outliers final: 47 residues processed: 307 average time/residue: 0.2655 time to fit residues: 106.4630 Evaluate side-chains 326 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 270 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 230 GLN Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain D residue 22 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 287 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS ** F 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10358 Z= 0.282 Angle : 0.768 11.931 14093 Z= 0.370 Chirality : 0.048 0.271 1631 Planarity : 0.005 0.043 1800 Dihedral : 9.858 80.722 1800 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.50 % Allowed : 24.98 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.75 (0.24), residues: 1216 helix: -1.22 (1.01), residues: 26 sheet: -0.57 (0.22), residues: 562 loop : -1.71 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP C 180 HIS 0.013 0.001 HIS E 148 PHE 0.015 0.002 PHE C 94 TYR 0.019 0.002 TYR D 253 ARG 0.004 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 272 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6276 (OUTLIER) cc_final: 0.6071 (p-80) REVERT: A 163 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7106 (ttt90) REVERT: A 166 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6483 (mp) REVERT: B 124 MET cc_start: 0.5903 (ppp) cc_final: 0.5311 (ppp) REVERT: C 95 GLN cc_start: 0.7124 (mm-40) cc_final: 0.6874 (mm-40) REVERT: C 101 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6515 (ttt90) REVERT: C 167 MET cc_start: 0.6640 (mmm) cc_final: 0.6361 (mmm) REVERT: C 253 TYR cc_start: 0.7895 (OUTLIER) cc_final: 0.7643 (m-10) REVERT: C 265 LYS cc_start: 0.8119 (tmtt) cc_final: 0.7748 (tmtt) REVERT: D 51 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5697 (pt0) REVERT: D 100 VAL cc_start: 0.7661 (m) cc_final: 0.7424 (p) REVERT: D 250 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7678 (mm) REVERT: E 98 TRP cc_start: 0.6982 (p90) cc_final: 0.5774 (p90) REVERT: E 143 ARG cc_start: 0.6777 (mtp85) cc_final: 0.5971 (mmp80) REVERT: F 143 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6779 (mpt180) REVERT: F 156 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7463 (mm-30) REVERT: F 212 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5651 (tt) REVERT: F 217 LEU cc_start: -0.4928 (OUTLIER) cc_final: -0.5980 (tp) REVERT: F 270 LEU cc_start: -0.5802 (OUTLIER) cc_final: -0.6096 (mp) outliers start: 61 outliers final: 48 residues processed: 299 average time/residue: 0.2699 time to fit residues: 104.9816 Evaluate side-chains 330 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 272 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain C residue 253 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 175 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10358 Z= 0.269 Angle : 0.772 11.774 14093 Z= 0.369 Chirality : 0.047 0.274 1631 Planarity : 0.005 0.045 1800 Dihedral : 9.703 77.706 1800 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 6.22 % Allowed : 24.35 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.71 (0.24), residues: 1216 helix: -1.27 (1.02), residues: 26 sheet: -0.52 (0.23), residues: 546 loop : -1.69 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 180 HIS 0.016 0.001 HIS E 148 PHE 0.014 0.001 PHE C 94 TYR 0.019 0.002 TYR D 253 ARG 0.004 0.000 ARG D 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 277 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.6083 (p-80) REVERT: A 163 ARG cc_start: 0.7632 (tpp80) cc_final: 0.7100 (ttt90) REVERT: A 166 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6481 (mp) REVERT: B 124 MET cc_start: 0.5880 (ppp) cc_final: 0.5232 (ppp) REVERT: C 95 GLN cc_start: 0.7133 (mm-40) cc_final: 0.6878 (mm-40) REVERT: C 101 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6516 (ttt90) REVERT: C 167 MET cc_start: 0.6638 (mmm) cc_final: 0.6420 (mmm) REVERT: C 265 LYS cc_start: 0.8090 (tmtt) cc_final: 0.7745 (tmtt) REVERT: D 51 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5683 (pt0) REVERT: D 100 VAL cc_start: 0.7674 (m) cc_final: 0.7435 (p) REVERT: D 250 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7681 (mm) REVERT: E 98 TRP cc_start: 0.6985 (p90) cc_final: 0.5809 (p90) REVERT: E 143 ARG cc_start: 0.6819 (mtp85) cc_final: 0.6083 (mmp80) REVERT: F 68 LEU cc_start: 0.5065 (OUTLIER) cc_final: 0.4314 (pp) REVERT: F 124 ARG cc_start: 0.4402 (OUTLIER) cc_final: 0.4053 (tmt170) REVERT: F 136 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.6982 (mmp80) REVERT: F 143 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6764 (mpt180) REVERT: F 156 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7488 (mm-30) REVERT: F 212 LEU cc_start: 0.5842 (OUTLIER) cc_final: 0.5614 (tt) REVERT: F 217 LEU cc_start: -0.4824 (OUTLIER) cc_final: -0.5887 (tp) REVERT: F 270 LEU cc_start: -0.5766 (OUTLIER) cc_final: -0.6060 (mp) outliers start: 69 outliers final: 48 residues processed: 307 average time/residue: 0.2825 time to fit residues: 113.2972 Evaluate side-chains 333 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 273 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 101 ARG Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 122 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 175 HIS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 162 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6317 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10358 Z= 0.208 Angle : 0.744 11.257 14093 Z= 0.351 Chirality : 0.046 0.280 1631 Planarity : 0.005 0.042 1800 Dihedral : 9.337 73.979 1800 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 5.32 % Allowed : 25.34 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.62 (0.24), residues: 1216 helix: -1.27 (1.03), residues: 26 sheet: -0.48 (0.23), residues: 538 loop : -1.58 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 180 HIS 0.018 0.001 HIS E 148 PHE 0.015 0.001 PHE C 94 TYR 0.021 0.002 TYR D 253 ARG 0.004 0.000 ARG A 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 268 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6336 (OUTLIER) cc_final: 0.6035 (p-80) REVERT: A 160 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6516 (tmm-80) REVERT: A 163 ARG cc_start: 0.7586 (tpp80) cc_final: 0.7069 (ttt90) REVERT: A 166 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6393 (mp) REVERT: A 174 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6870 (mtm180) REVERT: B 124 MET cc_start: 0.5894 (ppp) cc_final: 0.5244 (ppp) REVERT: C 95 GLN cc_start: 0.7107 (mm-40) cc_final: 0.6854 (mm-40) REVERT: C 265 LYS cc_start: 0.8043 (tmtt) cc_final: 0.7642 (tmtt) REVERT: D 51 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5501 (pt0) REVERT: D 193 THR cc_start: 0.8276 (m) cc_final: 0.7712 (p) REVERT: E 98 TRP cc_start: 0.6973 (p90) cc_final: 0.6004 (p90) REVERT: E 143 ARG cc_start: 0.6848 (mtp85) cc_final: 0.6596 (mmp80) REVERT: F 81 HIS cc_start: 0.7896 (t70) cc_final: 0.7607 (t70) REVERT: F 124 ARG cc_start: 0.4275 (OUTLIER) cc_final: 0.3987 (tmt170) REVERT: F 129 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7206 (m-80) REVERT: F 136 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7170 (mmp80) REVERT: F 143 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6955 (mpt180) REVERT: F 156 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7446 (mm-30) REVERT: F 212 LEU cc_start: 0.5836 (OUTLIER) cc_final: 0.5631 (tt) outliers start: 59 outliers final: 45 residues processed: 296 average time/residue: 0.2751 time to fit residues: 106.3825 Evaluate side-chains 320 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 265 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 251 THR Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 109 optimal weight: 0.0670 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 99 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10358 Z= 0.212 Angle : 0.744 11.204 14093 Z= 0.350 Chirality : 0.046 0.279 1631 Planarity : 0.005 0.048 1800 Dihedral : 9.177 72.276 1800 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 5.50 % Allowed : 25.07 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.58 (0.24), residues: 1216 helix: -1.29 (1.01), residues: 26 sheet: -0.49 (0.23), residues: 538 loop : -1.52 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 180 HIS 0.018 0.001 HIS E 148 PHE 0.014 0.001 PHE C 94 TYR 0.020 0.002 TYR D 253 ARG 0.005 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 265 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6358 (OUTLIER) cc_final: 0.6032 (p-80) REVERT: A 160 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6521 (tmm-80) REVERT: A 163 ARG cc_start: 0.7582 (tpp80) cc_final: 0.7113 (ttt90) REVERT: A 166 LEU cc_start: 0.7132 (OUTLIER) cc_final: 0.6391 (mp) REVERT: A 174 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6911 (mtm180) REVERT: B 124 MET cc_start: 0.5900 (ppp) cc_final: 0.5250 (ppp) REVERT: C 95 GLN cc_start: 0.7092 (mm-40) cc_final: 0.6834 (mm-40) REVERT: C 265 LYS cc_start: 0.7979 (tmtt) cc_final: 0.7691 (tmtt) REVERT: D 51 GLU cc_start: 0.6027 (OUTLIER) cc_final: 0.5506 (pt0) REVERT: D 193 THR cc_start: 0.8289 (m) cc_final: 0.7734 (p) REVERT: E 98 TRP cc_start: 0.6982 (p90) cc_final: 0.6086 (p90) REVERT: E 143 ARG cc_start: 0.6869 (mtp85) cc_final: 0.6651 (mmp80) REVERT: F 81 HIS cc_start: 0.7897 (t70) cc_final: 0.7613 (t70) REVERT: F 124 ARG cc_start: 0.4319 (OUTLIER) cc_final: 0.4043 (tmt170) REVERT: F 129 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: F 136 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7173 (mmp80) REVERT: F 143 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6707 (mpt180) REVERT: F 156 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7452 (mm-30) outliers start: 61 outliers final: 46 residues processed: 294 average time/residue: 0.2641 time to fit residues: 101.1240 Evaluate side-chains 317 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 262 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 0.0970 chunk 96 optimal weight: 0.0060 chunk 10 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10358 Z= 0.223 Angle : 0.759 11.179 14093 Z= 0.356 Chirality : 0.046 0.276 1631 Planarity : 0.005 0.052 1800 Dihedral : 9.069 73.019 1800 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 5.23 % Allowed : 24.98 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.60 (0.24), residues: 1216 helix: -1.19 (1.02), residues: 26 sheet: -0.52 (0.23), residues: 540 loop : -1.52 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 180 HIS 0.019 0.001 HIS E 148 PHE 0.013 0.001 PHE C 94 TYR 0.020 0.002 TYR D 253 ARG 0.006 0.000 ARG D 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2432 Ramachandran restraints generated. 1216 Oldfield, 0 Emsley, 1216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 260 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 HIS cc_start: 0.6358 (OUTLIER) cc_final: 0.6053 (p-80) REVERT: A 160 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6530 (tmm-80) REVERT: A 163 ARG cc_start: 0.7598 (tpp80) cc_final: 0.7122 (ttt90) REVERT: A 166 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6389 (mp) REVERT: A 174 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6924 (mtm180) REVERT: B 124 MET cc_start: 0.5903 (ppp) cc_final: 0.5262 (ppp) REVERT: C 95 GLN cc_start: 0.7072 (mm-40) cc_final: 0.6825 (mm-40) REVERT: C 208 MET cc_start: 0.6617 (mtm) cc_final: 0.6368 (mmm) REVERT: C 232 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.3871 (tpm170) REVERT: C 253 TYR cc_start: 0.7826 (m-80) cc_final: 0.7022 (m-10) REVERT: C 265 LYS cc_start: 0.7954 (tmtt) cc_final: 0.7690 (tmtt) REVERT: D 51 GLU cc_start: 0.6011 (OUTLIER) cc_final: 0.5461 (pt0) REVERT: D 193 THR cc_start: 0.8279 (m) cc_final: 0.7720 (p) REVERT: E 98 TRP cc_start: 0.6980 (p90) cc_final: 0.6070 (p90) REVERT: E 143 ARG cc_start: 0.6927 (mtp85) cc_final: 0.6681 (mmp80) REVERT: F 81 HIS cc_start: 0.7898 (t70) cc_final: 0.7636 (t70) REVERT: F 124 ARG cc_start: 0.4308 (OUTLIER) cc_final: 0.4048 (tmt170) REVERT: F 129 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.7186 (m-80) REVERT: F 136 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7150 (mmp80) REVERT: F 143 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6731 (mpt180) REVERT: F 156 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7536 (mm-30) REVERT: F 217 LEU cc_start: -0.5020 (OUTLIER) cc_final: -0.6094 (tp) outliers start: 58 outliers final: 46 residues processed: 285 average time/residue: 0.2729 time to fit residues: 101.9558 Evaluate side-chains 316 residues out of total 1132 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 259 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 160 ARG Chi-restraints excluded: chain A residue 166 LEU Chi-restraints excluded: chain A residue 174 ARG Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 232 ARG Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 66 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 165 HIS Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 265 LYS Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 34 ARG Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 102 THR Chi-restraints excluded: chain E residue 121 THR Chi-restraints excluded: chain E residue 162 HIS Chi-restraints excluded: chain E residue 176 GLN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 50 CYS Chi-restraints excluded: chain F residue 87 GLN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 113 GLU Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 124 ARG Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 136 ARG Chi-restraints excluded: chain F residue 143 ARG Chi-restraints excluded: chain F residue 163 HIS Chi-restraints excluded: chain F residue 175 HIS Chi-restraints excluded: chain F residue 192 VAL Chi-restraints excluded: chain F residue 217 LEU Chi-restraints excluded: chain F residue 265 ASN Chi-restraints excluded: chain F residue 281 VAL Chi-restraints excluded: chain F residue 300 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0060 chunk 96 optimal weight: 0.0060 chunk 40 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 85 optimal weight: 0.0170 chunk 5 optimal weight: 0.7980 overall best weight: 0.3050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 163 HIS F 175 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.198968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.154503 restraints weight = 17889.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.159498 restraints weight = 9532.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.162808 restraints weight = 5942.590| |-----------------------------------------------------------------------------| r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10358 Z= 0.193 Angle : 0.745 11.106 14093 Z= 0.347 Chirality : 0.046 0.280 1631 Planarity : 0.005 0.051 1800 Dihedral : 8.834 72.250 1800 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 5.14 % Allowed : 25.43 % Favored : 69.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.54 (0.24), residues: 1216 helix: -1.20 (1.01), residues: 26 sheet: -0.47 (0.22), residues: 543 loop : -1.49 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 180 HIS 0.018 0.001 HIS E 148 PHE 0.012 0.001 PHE C 94 TYR 0.025 0.001 TYR D 253 ARG 0.005 0.000 ARG C 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2858.00 seconds wall clock time: 51 minutes 37.30 seconds (3097.30 seconds total)