Starting phenix.real_space_refine on Tue Feb 13 18:50:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmk_27542/02_2024/8dmk_27542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmk_27542/02_2024/8dmk_27542.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/8dmk_27542/02_2024/8dmk_27542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmk_27542/02_2024/8dmk_27542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmk_27542/02_2024/8dmk_27542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmk_27542/02_2024/8dmk_27542.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= 0.000 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 64 5.16 5 C 4601 2.51 5 N 1278 2.21 5 O 1404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 332": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 41": "OD1" <-> "OD2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 245": "OD1" <-> "OD2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 158": "OE1" <-> "OE2" Residue "G TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 200": "OE1" <-> "OE2" Residue "G ASP 207": "OD1" <-> "OD2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 334": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7348 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2432 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 22, 'TRANS': 282} Chain: "B" Number of atoms: 2454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2454 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 16, 'TRANS': 290} Chain: "G" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2391 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 16, 'TRANS': 288} Chain: "A" 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: "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: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.35, per 1000 atoms: 0.59 Number of scatterers: 7348 At special positions: 0 Unit cell: (69.012, 122.472, 110.808, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 64 16.00 O 1404 8.00 N 1278 7.00 C 4601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 166 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 312 " distance=2.03 Simple disulfide: pdb=" SG CYS A 311 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 35 " distance=2.03 Simple disulfide: pdb=" SG CYS B 56 " - pdb=" SG CYS B 79 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 76 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 190 " distance=2.03 Simple disulfide: pdb=" SG CYS B 271 " - pdb=" SG CYS B 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 273 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 312 " - pdb=" SG CYS B 332 " distance=2.03 Simple disulfide: pdb=" SG CYS G 69 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 77 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 182 " - pdb=" SG CYS G 205 " distance=2.03 Simple disulfide: pdb=" SG CYS G 286 " - pdb=" SG CYS G 295 " distance=2.03 Simple disulfide: pdb=" SG CYS G 288 " - pdb=" SG CYS G 305 " distance=2.03 Simple disulfide: pdb=" SG CYS G 307 " - pdb=" SG CYS G 316 " distance=2.03 Simple disulfide: pdb=" SG CYS G 319 " - pdb=" SG CYS G 339 " 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 NAG-ASN " NAG A 401 " - " ASN A 45 " " NAG A 402 " - " ASN A 79 " " NAG B 401 " - " ASN B 120 " " NAG G 401 " - " ASN G 60 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1714 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 12.2% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 162 through 169 removed outlier: 3.881A pdb=" N LEU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 226 removed outlier: 3.951A pdb=" N GLU A 224 " --> pdb=" O PRO A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.794A pdb=" N THR A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Processing helix chain 'B' and resid 104 through 110 removed outlier: 4.484A pdb=" N LEU B 108 " --> pdb=" O PRO B 105 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 110 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 221 through 226 Processing helix chain 'B' and resid 254 through 258 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.108A pdb=" N VAL G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR G 83 " --> pdb=" O THR G 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 79 through 83' Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 181 through 186 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 237 through 245 removed outlier: 3.721A pdb=" N THR G 245 " --> pdb=" O GLN G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 264 removed outlier: 4.178A pdb=" N VAL G 263 " --> pdb=" O GLY G 260 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 271 Processing helix chain 'G' and resid 321 through 324 removed outlier: 3.971A pdb=" N ASN G 324 " --> pdb=" O PRO G 321 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 321 through 324' Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35 removed outlier: 4.452A pdb=" N LEU A 34 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 275 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLY A 274 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 231 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 120 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ARG A 229 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 11.066A pdb=" N GLN A 122 " --> pdb=" O SER A 227 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N SER A 227 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 147 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 231 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU A 145 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LEU A 233 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 143 " --> pdb=" O LEU A 233 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU A 235 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN A 141 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TRP A 142 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TYR A 158 " --> pdb=" O TRP A 142 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A 144 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR A 190 " --> pdb=" O TRP A 156 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A 158 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 57 Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 101 removed outlier: 3.559A pdb=" N TRP A 100 " --> pdb=" O ILE A 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 288 through 289 removed outlier: 3.644A pdb=" N GLN A 294 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 40 through 41 removed outlier: 3.725A pdb=" N VAL B 262 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP B 112 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 40 through 41 removed outlier: 6.669A pdb=" N THR B 139 " --> pdb=" O TYR B 263 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N MET B 265 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 137 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL B 267 " --> pdb=" O HIS B 135 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N HIS B 135 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N MET B 138 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 50 through 52 removed outlier: 4.167A pdb=" N SER B 51 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 124 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 149 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 238 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA B 147 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N MET B 148 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N TYR B 165 " --> pdb=" O MET B 148 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 150 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N ASP B 191 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR B 165 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AB1, first strand: chain 'G' and resid 63 through 65 removed outlier: 11.634A pdb=" N LEU G 135 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N ASN G 254 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 12.939A pdb=" N LEU G 137 " --> pdb=" O THR G 252 " (cutoff:3.500A) removed outlier: 11.869A pdb=" N THR G 252 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 12.403A pdb=" N LEU G 139 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 13.058A pdb=" N SER G 250 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N LYS G 141 " --> pdb=" O ASP G 248 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ASP G 248 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER G 159 " --> pdb=" O ASN G 254 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N PHE G 160 " --> pdb=" O TYR G 177 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N TYR G 177 " --> pdb=" O PHE G 160 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE G 162 " --> pdb=" O TYR G 175 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N TYR G 175 " --> pdb=" O LEU G 204 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N THR G 206 " --> pdb=" O TYR G 175 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR G 177 " --> pdb=" O THR G 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 74 through 75 removed outlier: 4.380A pdb=" N GLU G 74 " --> pdb=" O CYS G 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 118 through 119 removed outlier: 3.823A pdb=" N ASP G 279 " --> pdb=" O LYS G 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR G 147 " --> pdb=" O GLY G 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 292 through 297 removed outlier: 5.243A pdb=" N GLU G 294 " --> pdb=" O ASN G 306 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL G 304 " --> pdb=" O MET G 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 311 through 312 removed outlier: 4.199A pdb=" N LYS G 318 " --> pdb=" O TYR G 312 " (cutoff:3.500A) 106 hydrogen bonds defined for protein. 237 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: 1.80 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2440 1.34 - 1.46: 1818 1.46 - 1.58: 3204 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 7541 Sorted by residual: bond pdb=" C1 NAG A 402 " pdb=" O5 NAG A 402 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C1 NAG B 401 " pdb=" O5 NAG B 401 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.90e+00 bond pdb=" C1 NAG G 401 " pdb=" O5 NAG G 401 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C SER G 213 " pdb=" N PRO G 214 " ideal model delta sigma weight residual 1.336 1.351 -0.015 1.20e-02 6.94e+03 1.60e+00 bond pdb=" CD2 HIS B 135 " pdb=" NE2 HIS B 135 " ideal model delta sigma weight residual 1.374 1.361 0.013 1.10e-02 8.26e+03 1.47e+00 ... (remaining 7536 not shown) Histogram of bond angle deviations from ideal: 99.56 - 106.45: 277 106.45 - 113.34: 3974 113.34 - 120.23: 2631 120.23 - 127.12: 3251 127.12 - 134.02: 115 Bond angle restraints: 10248 Sorted by residual: angle pdb=" CA CYS A 73 " pdb=" CB CYS A 73 " pdb=" SG CYS A 73 " ideal model delta sigma weight residual 114.40 122.86 -8.46 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CB MET B 148 " pdb=" CG MET B 148 " pdb=" SD MET B 148 " ideal model delta sigma weight residual 112.70 120.80 -8.10 3.00e+00 1.11e-01 7.29e+00 angle pdb=" CA GLU B 128 " pdb=" CB GLU B 128 " pdb=" CG GLU B 128 " ideal model delta sigma weight residual 114.10 109.19 4.91 2.00e+00 2.50e-01 6.04e+00 angle pdb=" N VAL G 78 " pdb=" CA VAL G 78 " pdb=" C VAL G 78 " ideal model delta sigma weight residual 108.82 106.11 2.71 1.22e+00 6.72e-01 4.93e+00 angle pdb=" CG1 ILE A 271 " pdb=" CB ILE A 271 " pdb=" CG2 ILE A 271 " ideal model delta sigma weight residual 110.70 104.30 6.40 3.00e+00 1.11e-01 4.55e+00 ... (remaining 10243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 4091 17.47 - 34.94: 411 34.94 - 52.41: 94 52.41 - 69.88: 14 69.88 - 87.35: 13 Dihedral angle restraints: 4623 sinusoidal: 1953 harmonic: 2670 Sorted by residual: dihedral pdb=" CB CYS B 65 " pdb=" SG CYS B 65 " pdb=" SG CYS B 76 " pdb=" CB CYS B 76 " ideal model delta sinusoidal sigma weight residual -86.00 -2.33 -83.67 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS A 277 " pdb=" SG CYS A 277 " pdb=" SG CYS A 286 " pdb=" CB CYS A 286 " ideal model delta sinusoidal sigma weight residual 93.00 166.70 -73.70 1 1.00e+01 1.00e-02 6.90e+01 dihedral pdb=" CB CYS A 279 " pdb=" SG CYS A 279 " pdb=" SG CYS A 297 " pdb=" CB CYS A 297 " ideal model delta sinusoidal sigma weight residual 93.00 152.87 -59.87 1 1.00e+01 1.00e-02 4.78e+01 ... (remaining 4620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 954 0.060 - 0.121: 133 0.121 - 0.181: 10 0.181 - 0.241: 1 0.241 - 0.301: 1 Chirality restraints: 1099 Sorted by residual: chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 79 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CB ILE A 271 " pdb=" CA ILE A 271 " pdb=" CG1 ILE A 271 " pdb=" CG2 ILE A 271 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA VAL G 78 " pdb=" N VAL G 78 " pdb=" C VAL G 78 " pdb=" CB VAL G 78 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 1096 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 71 " 0.040 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO G 72 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 72 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 72 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 60 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C VAL A 60 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL A 60 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU A 61 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG A 66 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 67 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 67 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 67 " -0.022 5.00e-02 4.00e+02 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 1 2.12 - 2.81: 2296 2.81 - 3.51: 10254 3.51 - 4.20: 17825 4.20 - 4.90: 29420 Nonbonded interactions: 59796 Sorted by model distance: nonbonded pdb=" OD2 ASP G 108 " pdb=" OG1 THR G 116 " model vdw 1.425 2.440 nonbonded pdb=" O ARG A 69 " pdb=" OH TYR G 109 " model vdw 2.154 2.440 nonbonded pdb=" OE2 GLU A 203 " pdb=" OG SER B 200 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR B 102 " pdb=" OG1 THR G 80 " model vdw 2.196 2.440 nonbonded pdb=" NH1 ARG A 263 " pdb=" OH TYR G 147 " model vdw 2.217 2.520 ... (remaining 59791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.310 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: 0.000 Extract box with map and model: 5.940 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.800 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7541 Z= 0.175 Angle : 0.570 8.462 10248 Z= 0.305 Chirality : 0.044 0.301 1099 Planarity : 0.004 0.059 1342 Dihedral : 14.545 87.345 2840 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.28), residues: 911 helix: -2.84 (0.52), residues: 59 sheet: -0.45 (0.48), residues: 135 loop : -0.69 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 172 HIS 0.005 0.001 HIS A 62 PHE 0.025 0.001 PHE A 56 TYR 0.019 0.001 TYR B 263 ARG 0.009 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.7276 (p90) cc_final: 0.6993 (p90) REVERT: B 259 TYR cc_start: 0.7935 (p90) cc_final: 0.7723 (p90) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1943 time to fit residues: 23.4467 Evaluate side-chains 69 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 37 optimal weight: 0.0050 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 52 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 ASN G 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7541 Z= 0.260 Angle : 0.607 9.475 10248 Z= 0.307 Chirality : 0.045 0.355 1099 Planarity : 0.004 0.040 1342 Dihedral : 5.799 59.411 1114 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.87 % Allowed : 8.60 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.28), residues: 911 helix: -2.79 (0.47), residues: 75 sheet: -0.75 (0.44), residues: 139 loop : -0.78 (0.24), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 117 HIS 0.006 0.001 HIS A 62 PHE 0.018 0.002 PHE A 56 TYR 0.024 0.002 TYR G 175 ARG 0.004 0.000 ARG A 263 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: B 230 ILE cc_start: 0.6819 (mm) cc_final: 0.6540 (mm) REVERT: B 259 TYR cc_start: 0.8144 (p90) cc_final: 0.7928 (p90) outliers start: 7 outliers final: 4 residues processed: 78 average time/residue: 0.1898 time to fit residues: 20.6498 Evaluate side-chains 74 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 261 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 112 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7541 Z= 0.357 Angle : 0.666 9.585 10248 Z= 0.344 Chirality : 0.046 0.369 1099 Planarity : 0.005 0.043 1342 Dihedral : 6.015 56.870 1114 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 24.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.24 % Allowed : 13.59 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.28), residues: 911 helix: -2.67 (0.49), residues: 69 sheet: -1.11 (0.44), residues: 139 loop : -1.02 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 113 HIS 0.011 0.002 HIS B 135 PHE 0.012 0.002 PHE B 77 TYR 0.021 0.002 TYR G 175 ARG 0.005 0.001 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: B 160 TRP cc_start: 0.6033 (m100) cc_final: 0.5828 (m100) REVERT: B 230 ILE cc_start: 0.6972 (mm) cc_final: 0.6731 (mm) outliers start: 18 outliers final: 12 residues processed: 81 average time/residue: 0.1872 time to fit residues: 20.9718 Evaluate side-chains 74 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 112 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7541 Z= 0.212 Angle : 0.576 9.517 10248 Z= 0.291 Chirality : 0.045 0.356 1099 Planarity : 0.004 0.038 1342 Dihedral : 5.725 57.017 1114 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 1.87 % Allowed : 15.96 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.28), residues: 911 helix: -2.87 (0.46), residues: 75 sheet: -1.18 (0.45), residues: 146 loop : -0.99 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.013 0.001 HIS A 301 PHE 0.011 0.001 PHE B 237 TYR 0.022 0.001 TYR G 175 ARG 0.003 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 290 GLU cc_start: 0.6149 (mm-30) cc_final: 0.5923 (mm-30) REVERT: B 135 HIS cc_start: 0.7909 (p-80) cc_final: 0.7477 (p90) REVERT: B 230 ILE cc_start: 0.7137 (mm) cc_final: 0.6875 (mm) outliers start: 15 outliers final: 10 residues processed: 84 average time/residue: 0.1838 time to fit residues: 21.7575 Evaluate side-chains 73 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 63 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.0010 chunk 17 optimal weight: 5.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 301 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7541 Z= 0.223 Angle : 0.576 9.189 10248 Z= 0.291 Chirality : 0.044 0.361 1099 Planarity : 0.004 0.039 1342 Dihedral : 5.517 56.818 1114 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.12 % Allowed : 17.08 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.27), residues: 911 helix: -2.80 (0.46), residues: 75 sheet: -1.07 (0.46), residues: 136 loop : -1.08 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 111 HIS 0.006 0.001 HIS A 301 PHE 0.011 0.001 PHE B 237 TYR 0.016 0.001 TYR G 175 ARG 0.003 0.000 ARG B 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 67 time to evaluate : 0.876 Fit side-chains REVERT: B 230 ILE cc_start: 0.7204 (mm) cc_final: 0.6922 (mm) outliers start: 25 outliers final: 13 residues processed: 84 average time/residue: 0.1845 time to fit residues: 21.6268 Evaluate side-chains 75 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS ** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7541 Z= 0.165 Angle : 0.573 9.059 10248 Z= 0.288 Chirality : 0.045 0.350 1099 Planarity : 0.004 0.038 1342 Dihedral : 5.259 59.942 1114 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.74 % Allowed : 17.71 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.27), residues: 911 helix: -3.13 (0.44), residues: 74 sheet: -0.99 (0.49), residues: 126 loop : -1.06 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 320 HIS 0.011 0.001 HIS A 301 PHE 0.011 0.001 PHE B 237 TYR 0.013 0.001 TYR G 175 ARG 0.005 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 70 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: B 163 TYR cc_start: 0.8661 (OUTLIER) cc_final: 0.8407 (m-10) REVERT: B 230 ILE cc_start: 0.7144 (mm) cc_final: 0.6863 (mm) outliers start: 22 outliers final: 15 residues processed: 87 average time/residue: 0.1779 time to fit residues: 21.9621 Evaluate side-chains 81 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 65 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 70 HIS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 4.9990 chunk 49 optimal weight: 0.0040 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 51 optimal weight: 1.9990 overall best weight: 1.0136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 HIS A 318 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7541 Z= 0.175 Angle : 0.577 9.132 10248 Z= 0.287 Chirality : 0.044 0.356 1099 Planarity : 0.004 0.038 1342 Dihedral : 5.141 59.675 1114 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.62 % Allowed : 19.58 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.28), residues: 911 helix: -2.92 (0.48), residues: 67 sheet: -0.84 (0.50), residues: 124 loop : -1.04 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.008 0.001 HIS B 135 PHE 0.009 0.001 PHE B 143 TYR 0.023 0.001 TYR G 175 ARG 0.006 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 66 time to evaluate : 0.866 Fit side-chains REVERT: B 163 TYR cc_start: 0.8595 (OUTLIER) cc_final: 0.8305 (m-10) REVERT: B 230 ILE cc_start: 0.7101 (mm) cc_final: 0.6839 (mm) outliers start: 21 outliers final: 17 residues processed: 83 average time/residue: 0.1717 time to fit residues: 20.3880 Evaluate side-chains 81 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 63 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 76 CYS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 181 SER Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.0570 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 55 optimal weight: 8.9990 chunk 59 optimal weight: 0.0270 chunk 42 optimal weight: 10.0000 chunk 8 optimal weight: 0.0870 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 75 optimal weight: 7.9990 overall best weight: 0.3334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7541 Z= 0.144 Angle : 0.561 8.924 10248 Z= 0.276 Chirality : 0.044 0.345 1099 Planarity : 0.004 0.038 1342 Dihedral : 4.820 56.013 1114 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.62 % Allowed : 20.32 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.28), residues: 911 helix: -2.91 (0.48), residues: 67 sheet: -0.77 (0.50), residues: 124 loop : -0.96 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 320 HIS 0.007 0.001 HIS B 135 PHE 0.007 0.001 PHE B 237 TYR 0.017 0.001 TYR G 175 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 70 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: B 163 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8405 (m-10) REVERT: B 230 ILE cc_start: 0.7163 (mm) cc_final: 0.6877 (mm) REVERT: G 117 TRP cc_start: 0.8423 (p90) cc_final: 0.8159 (p90) outliers start: 13 outliers final: 12 residues processed: 80 average time/residue: 0.1848 time to fit residues: 21.0113 Evaluate side-chains 80 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 163 TYR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7541 Z= 0.208 Angle : 0.593 9.083 10248 Z= 0.293 Chirality : 0.044 0.363 1099 Planarity : 0.004 0.040 1342 Dihedral : 5.014 58.005 1114 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.49 % Allowed : 19.95 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.28), residues: 911 helix: -2.52 (0.53), residues: 60 sheet: -0.87 (0.50), residues: 121 loop : -0.98 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 100 HIS 0.009 0.001 HIS B 135 PHE 0.007 0.001 PHE B 237 TYR 0.026 0.001 TYR G 175 ARG 0.004 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.911 Fit side-chains REVERT: A 100 TRP cc_start: 0.6418 (p-90) cc_final: 0.6085 (p-90) REVERT: B 230 ILE cc_start: 0.7063 (mm) cc_final: 0.6799 (mm) outliers start: 20 outliers final: 15 residues processed: 79 average time/residue: 0.1588 time to fit residues: 18.4439 Evaluate side-chains 76 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 HIS Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 0.2980 chunk 89 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7541 Z= 0.190 Angle : 0.592 9.410 10248 Z= 0.290 Chirality : 0.045 0.355 1099 Planarity : 0.004 0.040 1342 Dihedral : 5.034 58.803 1114 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.00 % Allowed : 20.70 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.28), residues: 911 helix: -2.55 (0.53), residues: 60 sheet: -0.70 (0.51), residues: 117 loop : -1.00 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 100 HIS 0.009 0.001 HIS B 135 PHE 0.013 0.001 PHE B 207 TYR 0.025 0.001 TYR G 175 ARG 0.005 0.000 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 62 time to evaluate : 0.945 Fit side-chains REVERT: B 230 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6864 (mm) outliers start: 16 outliers final: 13 residues processed: 74 average time/residue: 0.1648 time to fit residues: 17.8775 Evaluate side-chains 75 residues out of total 802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 156 TRP Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain B residue 65 CYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 106 ASN Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 129 TYR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 261 ASP Chi-restraints excluded: chain G residue 312 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN A 112 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.115160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.093807 restraints weight = 22593.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.096976 restraints weight = 13230.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.099103 restraints weight = 9131.778| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7541 Z= 0.192 Angle : 0.598 9.291 10248 Z= 0.292 Chirality : 0.045 0.357 1099 Planarity : 0.004 0.041 1342 Dihedral : 5.037 58.670 1114 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 2.24 % Allowed : 21.20 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.28), residues: 911 helix: -2.47 (0.54), residues: 60 sheet: -0.70 (0.50), residues: 117 loop : -1.03 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 113 HIS 0.008 0.001 HIS B 135 PHE 0.012 0.001 PHE B 207 TYR 0.025 0.001 TYR G 175 ARG 0.005 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1634.09 seconds wall clock time: 31 minutes 4.66 seconds (1864.66 seconds total)