Starting phenix.real_space_refine on Sun Aug 4 00:39:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wz2_37944/08_2024/8wz2_37944.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wz2_37944/08_2024/8wz2_37944.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wz2_37944/08_2024/8wz2_37944.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wz2_37944/08_2024/8wz2_37944.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wz2_37944/08_2024/8wz2_37944.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wz2_37944/08_2024/8wz2_37944.cif" } resolution = 2.73 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= 0.028 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 65 5.16 5 C 5956 2.51 5 N 1605 2.21 5 O 1729 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 121": "NH1" <-> "NH2" Residue "R PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 72": "NH1" <-> "NH2" Residue "R PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 160": "NH1" <-> "NH2" Residue "R PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9355 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "L" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 147 Classifications: {'peptide': 26} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 24} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2528 Classifications: {'peptide': 322} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 66 Time building chain proxies: 6.71, per 1000 atoms: 0.72 Number of scatterers: 9355 At special positions: 0 Unit cell: (115.34, 147.46, 127.02, 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 65 16.00 O 1729 8.00 N 1605 7.00 C 5956 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 118 " - pdb=" SG CYS R 201 " distance=1.89 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.67 Conformation dependent library (CDL) restraints added in 1.7 seconds 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 40.6% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.663A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.575A pdb=" N ASN A 238 " --> pdb=" O GLN A 234 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 243 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 279 removed outlier: 4.141A pdb=" N TYR A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.813A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 298 through 319 removed outlier: 4.246A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 removed outlier: 3.858A pdb=" N ARG A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.729A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.679A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 removed outlier: 3.616A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.701A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 47 removed outlier: 3.853A pdb=" N ASP G 47 " --> pdb=" O ALA G 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 44 through 47' Processing helix chain 'L' and resid 99 through 111 Processing helix chain 'R' and resid 10 through 19 removed outlier: 3.933A pdb=" N HIS R 18 " --> pdb=" O LEU R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 30 Processing helix chain 'R' and resid 41 through 72 Processing helix chain 'R' and resid 74 through 77 Processing helix chain 'R' and resid 78 through 108 removed outlier: 3.733A pdb=" N ILE R 82 " --> pdb=" O THR R 78 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE R 83 " --> pdb=" O VAL R 79 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE R 99 " --> pdb=" O THR R 95 " (cutoff:3.500A) Proline residue: R 100 - end of helix Processing helix chain 'R' and resid 116 through 149 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 149 through 157 removed outlier: 4.067A pdb=" N TRP R 155 " --> pdb=" O PHE R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 183 Proline residue: R 179 - end of helix removed outlier: 3.838A pdb=" N HIS R 182 " --> pdb=" O SER R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 223 removed outlier: 3.992A pdb=" N GLN R 211 " --> pdb=" O SER R 207 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS R 212 " --> pdb=" O PRO R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 243 Processing helix chain 'R' and resid 262 through 298 removed outlier: 3.759A pdb=" N TRP R 286 " --> pdb=" O PHE R 282 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.591A pdb=" N GLU R 297 " --> pdb=" O HIS R 293 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR R 298 " --> pdb=" O MET R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 removed outlier: 3.717A pdb=" N TYR R 305 " --> pdb=" O PHE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 323 Processing helix chain 'R' and resid 323 through 334 removed outlier: 3.657A pdb=" N CYS R 327 " --> pdb=" O SER R 323 " (cutoff:3.500A) Proline residue: R 329 - end of helix Processing helix chain 'R' and resid 336 through 344 removed outlier: 3.930A pdb=" N LEU R 344 " --> pdb=" O LYS R 340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.105A pdb=" N LEU A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE A 199 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.867A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.554A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.662A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 142 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.694A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.965A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.470A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B 256 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.309A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 7.130A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.713A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.713A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 184 through 191 removed outlier: 3.622A pdb=" N LEU R 202 " --> pdb=" O GLN R 185 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS R 196 " --> pdb=" O ASP R 191 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1356 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: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 1519 1.27 - 1.41: 2399 1.41 - 1.54: 5462 1.54 - 1.68: 67 1.68 - 1.81: 99 Bond restraints: 9546 Sorted by residual: bond pdb=" C GLU R 203 " pdb=" N GLU R 204 " ideal model delta sigma weight residual 1.331 1.578 -0.248 1.48e-02 4.57e+03 2.81e+02 bond pdb=" C ALA R 27 " pdb=" O ALA R 27 " ideal model delta sigma weight residual 1.236 1.136 0.100 1.15e-02 7.56e+03 7.62e+01 bond pdb=" C GLU R 23 " pdb=" O GLU R 23 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.26e-02 6.30e+03 2.76e+01 bond pdb=" CA THR R 37 " pdb=" C THR R 37 " ideal model delta sigma weight residual 1.528 1.469 0.059 1.18e-02 7.18e+03 2.51e+01 bond pdb=" CA ARG R 22 " pdb=" C ARG R 22 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.37e-02 5.33e+03 1.63e+01 ... (remaining 9541 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.55: 224 106.55 - 113.57: 5230 113.57 - 120.59: 3966 120.59 - 127.61: 3407 127.61 - 134.64: 104 Bond angle restraints: 12931 Sorted by residual: angle pdb=" O ILE R 199 " pdb=" C ILE R 199 " pdb=" N CYS R 200 " ideal model delta sigma weight residual 122.45 112.32 10.13 1.07e+00 8.73e-01 8.95e+01 angle pdb=" C ILE R 199 " pdb=" N CYS R 200 " pdb=" CA CYS R 200 " ideal model delta sigma weight residual 123.00 133.83 -10.83 1.38e+00 5.25e-01 6.16e+01 angle pdb=" N THR R 37 " pdb=" CA THR R 37 " pdb=" C THR R 37 " ideal model delta sigma weight residual 110.08 99.53 10.55 1.38e+00 5.25e-01 5.84e+01 angle pdb=" N ILE R 26 " pdb=" CA ILE R 26 " pdb=" C ILE R 26 " ideal model delta sigma weight residual 110.62 103.17 7.45 1.02e+00 9.61e-01 5.34e+01 angle pdb=" CA ILE R 199 " pdb=" C ILE R 199 " pdb=" N CYS R 200 " ideal model delta sigma weight residual 116.59 126.91 -10.32 1.44e+00 4.82e-01 5.13e+01 ... (remaining 12926 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5562 17.98 - 35.96: 91 35.96 - 53.94: 19 53.94 - 71.93: 4 71.93 - 89.91: 1 Dihedral angle restraints: 5677 sinusoidal: 2189 harmonic: 3488 Sorted by residual: dihedral pdb=" N GLN R 24 " pdb=" C GLN R 24 " pdb=" CA GLN R 24 " pdb=" CB GLN R 24 " ideal model delta harmonic sigma weight residual 122.80 132.29 -9.49 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" C GLN R 24 " pdb=" N GLN R 24 " pdb=" CA GLN R 24 " pdb=" CB GLN R 24 " ideal model delta harmonic sigma weight residual -122.60 -131.98 9.38 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB GLU R 39 " pdb=" CG GLU R 39 " pdb=" CD GLU R 39 " pdb=" OE1 GLU R 39 " ideal model delta sinusoidal sigma weight residual 0.00 89.91 -89.91 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 1468 0.340 - 0.679: 0 0.679 - 1.019: 0 1.019 - 1.359: 0 1.359 - 1.698: 3 Chirality restraints: 1471 Sorted by residual: chirality pdb=" CG LEU R 54 " pdb=" CB LEU R 54 " pdb=" CD1 LEU R 54 " pdb=" CD2 LEU R 54 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.21e+01 chirality pdb=" CB VAL R 79 " pdb=" CA VAL R 79 " pdb=" CG1 VAL R 79 " pdb=" CG2 VAL R 79 " both_signs ideal model delta sigma weight residual False -2.63 -1.12 -1.50 2.00e-01 2.50e+01 5.66e+01 chirality pdb=" CB VAL R 279 " pdb=" CA VAL R 279 " pdb=" CG1 VAL R 279 " pdb=" CG2 VAL R 279 " both_signs ideal model delta sigma weight residual False -2.63 -1.14 -1.49 2.00e-01 2.50e+01 5.56e+01 ... (remaining 1468 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 21 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C THR R 21 " -0.061 2.00e-02 2.50e+03 pdb=" O THR R 21 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG R 22 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 29 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C TYR R 29 " 0.043 2.00e-02 2.50e+03 pdb=" O TYR R 29 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG R 30 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 183 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C VAL R 183 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL R 183 " -0.013 2.00e-02 2.50e+03 pdb=" N GLN R 184 " -0.013 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 102 2.60 - 3.18: 8324 3.18 - 3.75: 14214 3.75 - 4.33: 20031 4.33 - 4.90: 33654 Nonbonded interactions: 76325 Sorted by model distance: nonbonded pdb=" O MET R 295 " pdb=" OG SER R 299 " model vdw 2.029 3.040 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.044 3.040 nonbonded pdb=" OH TYR R 190 " pdb=" OE1 GLU R 195 " model vdw 2.125 3.040 nonbonded pdb=" OG SER R 73 " pdb=" OD1 ASN R 342 " model vdw 2.134 3.040 nonbonded pdb=" O SER A 242 " pdb=" ND2 ASN A 246 " model vdw 2.137 3.120 ... (remaining 76320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.070 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: 0.640 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 29.950 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:16.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 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 : 0.004 0.248 9546 Z= 0.295 Angle : 0.580 11.132 12931 Z= 0.363 Chirality : 0.082 1.698 1471 Planarity : 0.002 0.035 1638 Dihedral : 7.423 89.908 3418 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % 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: -1.03 (0.23), residues: 1181 helix: 0.54 (0.24), residues: 420 sheet: -0.61 (0.30), residues: 265 loop : -1.76 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 181 HIS 0.012 0.001 HIS A 324 PHE 0.021 0.001 PHE B 239 TYR 0.024 0.001 TYR R 36 ARG 0.006 0.000 ARG L 121 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 410 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 235 ASN cc_start: 0.7658 (m-40) cc_final: 0.7291 (m-40) REVERT: B 251 ASP cc_start: 0.7324 (p0) cc_final: 0.7118 (p0) REVERT: R 207 SER cc_start: 0.7551 (t) cc_final: 0.6633 (t) outliers start: 1 outliers final: 2 residues processed: 410 average time/residue: 1.2526 time to fit residues: 544.7424 Evaluate side-chains 224 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain G residue 23 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.7980 chunk 89 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN B 273 ASN B 300 ASN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 167 HIS E 194 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 106 ASN R 125 GLN R 338 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9546 Z= 0.233 Angle : 0.636 7.485 12931 Z= 0.326 Chirality : 0.042 0.155 1471 Planarity : 0.005 0.112 1638 Dihedral : 4.306 96.281 1300 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.30 % Allowed : 19.08 % Favored : 77.62 % 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: -0.12 (0.24), residues: 1181 helix: 1.49 (0.24), residues: 427 sheet: -0.14 (0.31), residues: 265 loop : -1.48 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 46 HIS 0.007 0.002 HIS E 34 PHE 0.016 0.001 PHE A 189 TYR 0.021 0.001 TYR R 194 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 248 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLN cc_start: 0.8339 (tp40) cc_final: 0.7802 (tp40) REVERT: R 68 TYR cc_start: 0.7718 (t80) cc_final: 0.7423 (t80) REVERT: R 120 MET cc_start: 0.8041 (ttp) cc_final: 0.7653 (ppp) REVERT: R 187 GLU cc_start: 0.5732 (tm-30) cc_final: 0.5512 (tm-30) outliers start: 33 outliers final: 11 residues processed: 268 average time/residue: 1.2074 time to fit residues: 345.3146 Evaluate side-chains 218 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 chunk 115 optimal weight: 0.4980 chunk 95 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 186 GLN R 63 ASN R 290 HIS R 338 ASN R 342 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9546 Z= 0.213 Angle : 0.637 13.034 12931 Z= 0.321 Chirality : 0.042 0.190 1471 Planarity : 0.004 0.035 1638 Dihedral : 4.391 89.580 1300 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.00 % Allowed : 19.58 % Favored : 76.42 % 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: 0.32 (0.24), residues: 1181 helix: 1.80 (0.25), residues: 435 sheet: 0.01 (0.32), residues: 263 loop : -1.15 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.006 0.001 HIS E 34 PHE 0.018 0.001 PHE R 61 TYR 0.024 0.001 TYR B 64 ARG 0.008 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 230 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 17 GLN cc_start: 0.8647 (tp40) cc_final: 0.8420 (tp40) REVERT: G 21 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7897 (mt-10) REVERT: R 68 TYR cc_start: 0.7679 (t80) cc_final: 0.7191 (t80) REVERT: R 225 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8453 (mp) outliers start: 40 outliers final: 15 residues processed: 255 average time/residue: 1.2416 time to fit residues: 337.5877 Evaluate side-chains 218 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 202 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 196 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN E 186 GLN R 63 ASN R 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9546 Z= 0.207 Angle : 0.618 10.039 12931 Z= 0.315 Chirality : 0.042 0.176 1471 Planarity : 0.004 0.035 1638 Dihedral : 4.311 83.339 1300 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.90 % Allowed : 21.78 % Favored : 74.33 % 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: 0.48 (0.24), residues: 1181 helix: 1.92 (0.25), residues: 431 sheet: 0.11 (0.32), residues: 264 loop : -1.03 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.006 0.001 HIS R 198 PHE 0.021 0.001 PHE E 203 TYR 0.017 0.001 TYR R 157 ARG 0.009 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 215 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: B 239 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: G 13 LYS cc_start: 0.9200 (mmmm) cc_final: 0.8827 (mmmm) REVERT: R 74 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7742 (mmmt) REVERT: R 155 TRP cc_start: 0.8535 (p-90) cc_final: 0.8306 (p-90) REVERT: R 225 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8392 (tt) REVERT: R 270 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7941 (tpp80) outliers start: 39 outliers final: 16 residues processed: 237 average time/residue: 1.0521 time to fit residues: 266.0028 Evaluate side-chains 213 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 195 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 34 HIS E 186 GLN E 194 ASN R 63 ASN ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 9546 Z= 0.368 Angle : 0.665 9.234 12931 Z= 0.347 Chirality : 0.045 0.188 1471 Planarity : 0.004 0.038 1638 Dihedral : 4.081 20.767 1298 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.50 % Allowed : 21.98 % Favored : 73.53 % 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: 0.52 (0.24), residues: 1181 helix: 1.73 (0.25), residues: 428 sheet: 0.23 (0.32), residues: 270 loop : -0.82 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 87 HIS 0.006 0.002 HIS R 198 PHE 0.015 0.002 PHE R 61 TYR 0.020 0.002 TYR E 190 ARG 0.011 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 208 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6828 (ppp80) REVERT: B 239 PHE cc_start: 0.9282 (OUTLIER) cc_final: 0.8271 (m-80) REVERT: E 223 ASP cc_start: 0.7770 (m-30) cc_final: 0.7361 (m-30) REVERT: G 28 LYS cc_start: 0.8665 (mtpm) cc_final: 0.8302 (mtpm) REVERT: R 77 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7506 (mtt90) REVERT: R 270 ARG cc_start: 0.8353 (tpp80) cc_final: 0.8041 (tpp80) outliers start: 45 outliers final: 17 residues processed: 236 average time/residue: 1.2544 time to fit residues: 315.2126 Evaluate side-chains 213 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 190 TYR Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 200 CYS Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN E 194 ASN R 63 ASN ** R 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9546 Z= 0.219 Angle : 0.653 9.315 12931 Z= 0.338 Chirality : 0.043 0.185 1471 Planarity : 0.004 0.037 1638 Dihedral : 3.958 19.746 1298 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.30 % Allowed : 25.07 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.24), residues: 1181 helix: 1.79 (0.25), residues: 429 sheet: 0.27 (0.31), residues: 281 loop : -0.90 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.007 0.001 HIS R 198 PHE 0.016 0.001 PHE R 61 TYR 0.019 0.002 TYR R 68 ARG 0.010 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6793 (ppp80) REVERT: B 239 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8244 (m-80) REVERT: G 28 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8293 (mtpm) REVERT: R 77 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7157 (mtt90) REVERT: R 155 TRP cc_start: 0.8611 (p-90) cc_final: 0.8374 (p-90) REVERT: R 160 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7152 (tpm170) REVERT: R 225 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8468 (tt) REVERT: R 240 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7591 (pp20) REVERT: R 270 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8014 (tpp80) outliers start: 33 outliers final: 17 residues processed: 233 average time/residue: 1.2250 time to fit residues: 304.3850 Evaluate side-chains 215 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN R 63 ASN ** R 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.104 9546 Z= 0.645 Angle : 0.839 10.661 12931 Z= 0.442 Chirality : 0.052 0.240 1471 Planarity : 0.005 0.059 1638 Dihedral : 4.842 22.950 1298 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.90 % Allowed : 25.57 % Favored : 69.53 % 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: 0.24 (0.24), residues: 1181 helix: 1.12 (0.25), residues: 437 sheet: 0.41 (0.32), residues: 253 loop : -0.81 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 87 HIS 0.009 0.003 HIS G 43 PHE 0.018 0.002 PHE R 192 TYR 0.032 0.003 TYR E 190 ARG 0.007 0.001 ARG R 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8813 (ttpp) REVERT: A 247 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7223 (ppp80) REVERT: E 223 ASP cc_start: 0.7855 (m-30) cc_final: 0.7596 (m-30) REVERT: G 28 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8348 (mtpm) REVERT: R 77 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7237 (mtt90) REVERT: R 91 ASP cc_start: 0.8455 (t70) cc_final: 0.8241 (t70) REVERT: R 160 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7370 (tpm170) REVERT: R 187 GLU cc_start: 0.5546 (OUTLIER) cc_final: 0.4289 (tm-30) REVERT: R 269 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8118 (tptt) REVERT: R 270 ARG cc_start: 0.8478 (tpp80) cc_final: 0.8121 (tpp80) outliers start: 49 outliers final: 16 residues processed: 211 average time/residue: 1.4164 time to fit residues: 316.7054 Evaluate side-chains 198 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain G residue 23 ASN Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 121 VAL Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 187 GLU Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 197 HIS ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 ASN ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN R 342 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9546 Z= 0.232 Angle : 0.739 10.272 12931 Z= 0.378 Chirality : 0.044 0.185 1471 Planarity : 0.004 0.053 1638 Dihedral : 4.453 20.281 1298 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.10 % Allowed : 28.07 % Favored : 68.83 % 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: 0.46 (0.24), residues: 1181 helix: 1.52 (0.25), residues: 435 sheet: 0.37 (0.32), residues: 254 loop : -0.80 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 174 HIS 0.010 0.002 HIS R 198 PHE 0.014 0.001 PHE A 189 TYR 0.021 0.002 TYR R 68 ARG 0.011 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 202 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7099 (ppp80) REVERT: B 239 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8250 (m-80) REVERT: E 223 ASP cc_start: 0.7770 (m-30) cc_final: 0.7454 (m-30) REVERT: G 8 ILE cc_start: 0.9219 (pp) cc_final: 0.8573 (pp) REVERT: R 77 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7338 (mtt90) REVERT: R 160 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7267 (tpm170) REVERT: R 204 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7949 (mm-30) REVERT: R 225 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8486 (tt) REVERT: R 240 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7653 (pp20) REVERT: R 270 ARG cc_start: 0.8383 (tpp80) cc_final: 0.8043 (tpp80) outliers start: 31 outliers final: 13 residues processed: 224 average time/residue: 1.3217 time to fit residues: 314.7025 Evaluate side-chains 207 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 342 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 9546 Z= 0.319 Angle : 0.782 10.439 12931 Z= 0.406 Chirality : 0.046 0.189 1471 Planarity : 0.004 0.039 1638 Dihedral : 4.410 19.998 1296 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.40 % Allowed : 29.57 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.25), residues: 1181 helix: 1.49 (0.25), residues: 433 sheet: 0.36 (0.31), residues: 266 loop : -0.69 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 170 HIS 0.008 0.002 HIS R 198 PHE 0.013 0.001 PHE A 189 TYR 0.022 0.002 TYR R 36 ARG 0.011 0.001 ARG R 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 189 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7281 (ppp80) REVERT: B 239 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8174 (m-80) REVERT: E 223 ASP cc_start: 0.7812 (m-30) cc_final: 0.7337 (m-30) REVERT: R 77 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7291 (mtt90) REVERT: R 160 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7304 (tpm170) REVERT: R 240 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7748 (pp20) REVERT: R 270 ARG cc_start: 0.8405 (tpp80) cc_final: 0.8096 (tpp80) outliers start: 24 outliers final: 17 residues processed: 206 average time/residue: 1.2982 time to fit residues: 284.2502 Evaluate side-chains 202 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 GLN ** R 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 338 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.6495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9546 Z= 0.252 Angle : 0.802 12.519 12931 Z= 0.413 Chirality : 0.046 0.232 1471 Planarity : 0.004 0.080 1638 Dihedral : 4.391 19.575 1296 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.00 % Allowed : 29.87 % Favored : 68.13 % 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: 0.56 (0.25), residues: 1181 helix: 1.55 (0.25), residues: 427 sheet: 0.40 (0.32), residues: 260 loop : -0.65 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 205 HIS 0.008 0.001 HIS R 198 PHE 0.015 0.001 PHE R 61 TYR 0.021 0.001 TYR R 68 ARG 0.011 0.001 ARG G 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 192 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7244 (ppp80) REVERT: B 239 PHE cc_start: 0.9232 (OUTLIER) cc_final: 0.8181 (m-80) REVERT: G 12 ARG cc_start: 0.8318 (pmm-80) cc_final: 0.8001 (pmm-80) REVERT: R 77 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7384 (mtt90) REVERT: R 91 ASP cc_start: 0.8458 (t70) cc_final: 0.8076 (t70) REVERT: R 160 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7260 (tpm170) REVERT: R 225 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8473 (tt) REVERT: R 240 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7720 (pp20) REVERT: R 270 ARG cc_start: 0.8375 (tpp80) cc_final: 0.8069 (tpp80) outliers start: 20 outliers final: 16 residues processed: 206 average time/residue: 1.2702 time to fit residues: 278.2979 Evaluate side-chains 206 residues out of total 1039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 17 GLU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 299 CYS Chi-restraints excluded: chain E residue 20 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain G residue 16 GLU Chi-restraints excluded: chain R residue 77 ARG Chi-restraints excluded: chain R residue 116 PHE Chi-restraints excluded: chain R residue 160 ARG Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 199 ILE Chi-restraints excluded: chain R residue 225 LEU Chi-restraints excluded: chain R residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** R 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 328 ASN ** 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 = 0.3493 r_free = 0.3493 target = 0.091429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.065159 restraints weight = 21123.852| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 3.50 r_work: 0.2806 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.201 9546 Z= 0.404 Angle : 1.222 59.197 12931 Z= 0.653 Chirality : 0.046 0.335 1471 Planarity : 0.005 0.081 1638 Dihedral : 4.401 19.542 1296 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.20 % Allowed : 30.17 % Favored : 67.63 % Cbeta Deviations : 0.18 % 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: 0.51 (0.25), residues: 1181 helix: 1.48 (0.25), residues: 427 sheet: 0.40 (0.32), residues: 260 loop : -0.67 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP R 155 HIS 0.007 0.001 HIS R 198 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR E 235 ARG 0.011 0.001 ARG E 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5366.60 seconds wall clock time: 94 minutes 18.97 seconds (5658.97 seconds total)