Starting phenix.real_space_refine on Mon Mar 11 17:12:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/03_2024/7xwo_33497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/03_2024/7xwo_33497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/03_2024/7xwo_33497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/03_2024/7xwo_33497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/03_2024/7xwo_33497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/03_2024/7xwo_33497.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 60 5.16 5 C 5553 2.51 5 N 1499 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 79": "OD1" <-> "OD2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C ASP 259": "OD1" <-> "OD2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 61": "OD1" <-> "OD2" Residue "E ASP 72": "OD1" <-> "OD2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 108": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 311": "OE1" <-> "OE2" Residue "F ASP 314": "OD1" <-> "OD2" Residue "F ASP 321": "OD1" <-> "OD2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "G ASP 25": "OD1" <-> "OD2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8725 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2041 Classifications: {'peptide': 272} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain breaks: 3 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 219 Unresolved non-hydrogen dihedrals: 162 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 114 Chain: "C" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2568 Classifications: {'peptide': 336} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1760 Classifications: {'peptide': 230} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 1867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1867 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 410 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 79 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.22, per 1000 atoms: 0.60 Number of scatterers: 8725 At special positions: 0 Unit cell: (119.48, 118.656, 108.768, 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 60 16.00 O 1613 8.00 N 1499 7.00 C 5553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 13 sheets defined 32.4% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'B' and resid 29 through 48 removed outlier: 3.744A pdb=" N ALA B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU B 35 " --> pdb=" O TRP B 31 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 4.050A pdb=" N ILE B 55 " --> pdb=" O ASN B 51 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TRP B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE B 57 " --> pdb=" O ILE B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 86 removed outlier: 3.524A pdb=" N VAL B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 74 " --> pdb=" O TYR B 70 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 86 " --> pdb=" O MET B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 removed outlier: 3.745A pdb=" N VAL B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR B 93 " --> pdb=" O PHE B 89 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA B 94 " --> pdb=" O ASN B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 111 through 123 removed outlier: 3.506A pdb=" N ILE B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 131 through 136 Processing helix chain 'B' and resid 148 through 163 removed outlier: 3.686A pdb=" N VAL B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 168 removed outlier: 3.608A pdb=" N CYS B 167 " --> pdb=" O ALA B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.597A pdb=" N ILE B 202 " --> pdb=" O HIS B 198 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 226 removed outlier: 3.549A pdb=" N VAL B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 217 " --> pdb=" O MET B 213 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B 218 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 261 removed outlier: 3.578A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 256 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE B 259 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 269 through 271 No H-bonds generated for 'chain 'B' and resid 269 through 271' Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.648A pdb=" N LEU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.832A pdb=" N ASN B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) Proline residue: B 304 - end of helix removed outlier: 3.610A pdb=" N TYR B 307 " --> pdb=" O ASN B 303 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 310 " --> pdb=" O ILE B 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 29 removed outlier: 3.589A pdb=" N GLU C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'E' and resid 27 through 31 removed outlier: 3.563A pdb=" N SER E 30 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 25 removed outlier: 3.566A pdb=" N ARG F 15 " --> pdb=" O ALA F 11 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN F 22 " --> pdb=" O MET F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 32 Processing helix chain 'F' and resid 45 through 52 removed outlier: 3.519A pdb=" N ILE F 49 " --> pdb=" O GLY F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 245 Processing helix chain 'F' and resid 260 through 270 removed outlier: 4.089A pdb=" N GLU F 266 " --> pdb=" O ASP F 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 267 " --> pdb=" O LEU F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 298 through 319 removed outlier: 3.913A pdb=" N PHE F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 358 removed outlier: 3.574A pdb=" N ASP F 348 " --> pdb=" O ASN F 344 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG F 356 " --> pdb=" O GLN F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 21 removed outlier: 3.942A pdb=" N LEU G 14 " --> pdb=" O GLN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.624A pdb=" N ASP G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU G 36 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 52 through 56 removed outlier: 6.587A pdb=" N ILE C 343 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N THR C 55 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU C 341 " --> pdb=" O THR C 55 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 63 through 68 removed outlier: 3.934A pdb=" N ALA C 65 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU C 84 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA C 97 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE C 86 " --> pdb=" O VAL C 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 105 through 110 removed outlier: 5.935A pdb=" N CYS C 126 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU C 143 " --> pdb=" O CYS C 126 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 128 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 139 " --> pdb=" O ASN C 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 156 through 157 removed outlier: 4.095A pdb=" N PHE C 156 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 183 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ASP C 175 " --> pdb=" O GLN C 181 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLN C 181 " --> pdb=" O ASP C 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 192 through 197 removed outlier: 3.881A pdb=" N GLN C 225 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP C 217 " --> pdb=" O CYS C 223 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N CYS C 223 " --> pdb=" O ASP C 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 234 through 239 removed outlier: 3.528A pdb=" N MET C 267 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP C 259 " --> pdb=" O GLU C 265 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU C 265 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 278 through 283 removed outlier: 6.708A pdb=" N CYS C 299 " --> pdb=" O VAL C 312 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL C 312 " --> pdb=" O CYS C 299 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL C 301 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP C 308 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.594A pdb=" N SER E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.581A pdb=" N THR E 114 " --> pdb=" O TYR E 93 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 141 through 142 Processing sheet with id=AB2, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.681A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 184 through 190 removed outlier: 6.483A pdb=" N LEU F 34 " --> pdb=" O HIS F 197 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE F 199 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 36 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL F 201 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG F 35 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 222 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU F 37 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 224 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU F 39 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP F 226 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 184 through 190 removed outlier: 6.483A pdb=" N LEU F 34 " --> pdb=" O HIS F 197 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N PHE F 199 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 36 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL F 201 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ARG F 35 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 222 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU F 37 " --> pdb=" O ILE F 222 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL F 224 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU F 39 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASP F 226 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE F 257 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE F 223 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASN F 259 " --> pdb=" O PHE F 223 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 225 " --> pdb=" O ASN F 259 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 942 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: 2.65 Time building geometry restraints manager: 3.55 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: 2815 1.34 - 1.46: 2183 1.46 - 1.58: 3825 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 8912 Sorted by residual: bond pdb=" C SER B 164 " pdb=" N PRO B 165 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.22e+00 bond pdb=" CG LEU E 174 " pdb=" CD1 LEU E 174 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.06e+00 bond pdb=" N ARG C 155 " pdb=" CA ARG C 155 " ideal model delta sigma weight residual 1.457 1.436 0.021 1.06e-02 8.90e+03 3.97e+00 bond pdb=" CA ARG C 155 " pdb=" C ARG C 155 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.24e-02 6.50e+03 3.76e+00 bond pdb=" CB VAL C 192 " pdb=" CG1 VAL C 192 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.29e+00 ... (remaining 8907 not shown) Histogram of bond angle deviations from ideal: 95.70 - 103.37: 86 103.37 - 111.04: 3195 111.04 - 118.71: 3766 118.71 - 126.37: 4905 126.37 - 134.04: 143 Bond angle restraints: 12095 Sorted by residual: angle pdb=" C VAL E 149 " pdb=" N THR E 150 " pdb=" CA THR E 150 " ideal model delta sigma weight residual 120.68 126.72 -6.04 1.52e+00 4.33e-01 1.58e+01 angle pdb=" CA TYR E 235 " pdb=" CB TYR E 235 " pdb=" CG TYR E 235 " ideal model delta sigma weight residual 113.90 106.81 7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N TYR E 235 " pdb=" CA TYR E 235 " pdb=" C TYR E 235 " ideal model delta sigma weight residual 109.81 117.81 -8.00 2.21e+00 2.05e-01 1.31e+01 angle pdb=" C PRO E 40 " pdb=" N GLU E 41 " pdb=" CA GLU E 41 " ideal model delta sigma weight residual 122.46 127.51 -5.05 1.41e+00 5.03e-01 1.28e+01 ... (remaining 12090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 4757 17.51 - 35.02: 412 35.02 - 52.54: 78 52.54 - 70.05: 7 70.05 - 87.56: 8 Dihedral angle restraints: 5262 sinusoidal: 1979 harmonic: 3283 Sorted by residual: dihedral pdb=" CA SER C 165 " pdb=" C SER C 165 " pdb=" N SER C 166 " pdb=" CA SER C 166 " ideal model delta harmonic sigma weight residual 180.00 133.36 46.64 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA GLY C 315 " pdb=" C GLY C 315 " pdb=" N HIS C 316 " pdb=" CA HIS C 316 " ideal model delta harmonic sigma weight residual 180.00 146.42 33.58 0 5.00e+00 4.00e-02 4.51e+01 dihedral pdb=" CA LEU C 122 " pdb=" C LEU C 122 " pdb=" N ASP C 123 " pdb=" CA ASP C 123 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 5259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 934 0.052 - 0.104: 349 0.104 - 0.156: 73 0.156 - 0.208: 13 0.208 - 0.260: 4 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CB VAL B 183 " pdb=" CA VAL B 183 " pdb=" CG1 VAL B 183 " pdb=" CG2 VAL B 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR E 90 " pdb=" CA THR E 90 " pdb=" OG1 THR E 90 " pdb=" CG2 THR E 90 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1370 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 240 " -0.050 5.00e-02 4.00e+02 7.52e-02 9.04e+00 pdb=" N PRO C 241 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 241 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 241 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 303 " 0.050 5.00e-02 4.00e+02 7.50e-02 9.00e+00 pdb=" N PRO B 304 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 304 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 304 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 145 " 0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO B 146 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.040 5.00e-02 4.00e+02 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2376 2.80 - 3.32: 7105 3.32 - 3.85: 14535 3.85 - 4.37: 16936 4.37 - 4.90: 29372 Nonbonded interactions: 70324 Sorted by model distance: nonbonded pdb=" OH TYR B 206 " pdb=" O ALA B 260 " model vdw 2.275 2.440 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.288 2.440 nonbonded pdb=" OG SER C 286 " pdb=" OD2 ASP G 47 " model vdw 2.306 2.440 nonbonded pdb=" OE2 GLU F 297 " pdb=" OG1 THR F 302 " model vdw 2.314 2.440 nonbonded pdb=" OG SER C 79 " pdb=" OD1 ASP C 81 " model vdw 2.320 2.440 ... (remaining 70319 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 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.840 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.990 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 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 : 0.007 0.067 8912 Z= 0.456 Angle : 0.868 11.295 12095 Z= 0.483 Chirality : 0.056 0.260 1373 Planarity : 0.008 0.075 1537 Dihedral : 13.885 87.562 3138 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.22 % Allowed : 6.09 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.88 (0.19), residues: 1108 helix: -4.90 (0.09), residues: 351 sheet: -1.51 (0.30), residues: 282 loop : -2.84 (0.22), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 156 HIS 0.008 0.002 HIS F 324 PHE 0.029 0.003 PHE B 284 TYR 0.042 0.003 TYR B 93 ARG 0.004 0.000 ARG G 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 213 time to evaluate : 0.929 Fit side-chains REVERT: B 28 MET cc_start: 0.4847 (mmm) cc_final: 0.4607 (mmm) REVERT: B 217 TYR cc_start: 0.7897 (m-80) cc_final: 0.7575 (m-80) REVERT: B 297 MET cc_start: 0.8391 (mmt) cc_final: 0.8062 (mmp) REVERT: C 75 LEU cc_start: 0.7854 (mt) cc_final: 0.7643 (mt) REVERT: C 160 ASN cc_start: 0.6271 (m-40) cc_final: 0.6065 (m-40) REVERT: C 308 ASP cc_start: 0.6858 (m-30) cc_final: 0.6654 (m-30) REVERT: E 85 LEU cc_start: 0.8692 (mm) cc_final: 0.8430 (mt) REVERT: F 239 ASP cc_start: 0.7125 (t0) cc_final: 0.6748 (t0) REVERT: F 247 ARG cc_start: 0.6815 (ttm110) cc_final: 0.6328 (ttm110) REVERT: F 250 ARG cc_start: 0.6798 (mtm-85) cc_final: 0.6552 (mtm-85) outliers start: 2 outliers final: 1 residues processed: 215 average time/residue: 1.0573 time to fit residues: 243.8019 Evaluate side-chains 190 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN C 115 ASN C 345 ASN E 167 HIS F 204 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8912 Z= 0.193 Angle : 0.559 6.873 12095 Z= 0.298 Chirality : 0.043 0.210 1373 Planarity : 0.005 0.055 1537 Dihedral : 5.489 33.716 1224 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.05 % Allowed : 13.60 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.22), residues: 1108 helix: -3.09 (0.20), residues: 347 sheet: -0.76 (0.30), residues: 279 loop : -2.23 (0.24), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 174 HIS 0.010 0.001 HIS E 167 PHE 0.038 0.001 PHE B 118 TYR 0.028 0.001 TYR E 235 ARG 0.005 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 197 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 28 MET cc_start: 0.4836 (mmm) cc_final: 0.4565 (mmm) REVERT: B 117 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6469 (ptm) REVERT: C 27 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7239 (mtt180) REVERT: C 186 THR cc_start: 0.8040 (p) cc_final: 0.7830 (p) REVERT: C 193 MET cc_start: 0.7971 (mmm) cc_final: 0.7618 (mmm) REVERT: C 308 ASP cc_start: 0.6863 (m-30) cc_final: 0.6640 (m-30) REVERT: E 85 LEU cc_start: 0.8668 (mm) cc_final: 0.8405 (mt) REVERT: F 247 ARG cc_start: 0.6934 (ttm110) cc_final: 0.6457 (ttm110) REVERT: F 250 ARG cc_start: 0.6773 (mtm-85) cc_final: 0.6527 (mtm-85) REVERT: F 262 ASP cc_start: 0.7146 (p0) cc_final: 0.6839 (p0) REVERT: F 276 GLU cc_start: 0.6666 (pm20) cc_final: 0.6328 (pm20) outliers start: 28 outliers final: 9 residues processed: 207 average time/residue: 1.2557 time to fit residues: 276.9665 Evaluate side-chains 196 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 313 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 89 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8912 Z= 0.252 Angle : 0.562 7.839 12095 Z= 0.297 Chirality : 0.044 0.220 1373 Planarity : 0.004 0.050 1537 Dihedral : 5.273 34.050 1224 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.70 % Allowed : 16.76 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.23), residues: 1108 helix: -1.93 (0.25), residues: 359 sheet: -0.51 (0.30), residues: 271 loop : -2.00 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 156 HIS 0.006 0.001 HIS F 329 PHE 0.026 0.002 PHE B 118 TYR 0.029 0.002 TYR E 235 ARG 0.006 0.000 ARG C 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 0.911 Fit side-chains REVERT: B 117 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6393 (ptm) REVERT: B 136 VAL cc_start: 0.7689 (OUTLIER) cc_final: 0.7428 (t) REVERT: C 79 SER cc_start: 0.7594 (p) cc_final: 0.7357 (p) REVERT: C 186 THR cc_start: 0.8063 (p) cc_final: 0.7846 (p) REVERT: C 193 MET cc_start: 0.7967 (mmm) cc_final: 0.7653 (mmm) REVERT: E 85 LEU cc_start: 0.8672 (mm) cc_final: 0.8394 (mt) REVERT: E 206 SER cc_start: 0.8035 (t) cc_final: 0.7810 (m) outliers start: 34 outliers final: 17 residues processed: 212 average time/residue: 1.1321 time to fit residues: 255.6501 Evaluate side-chains 208 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 282 HIS Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 267 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 48 optimal weight: 0.2980 chunk 67 optimal weight: 0.0870 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 109 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8912 Z= 0.189 Angle : 0.533 7.172 12095 Z= 0.279 Chirality : 0.043 0.201 1373 Planarity : 0.004 0.046 1537 Dihedral : 4.882 27.430 1224 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.03 % Allowed : 17.74 % Favored : 78.24 % 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: -1.87 (0.24), residues: 1108 helix: -1.10 (0.28), residues: 348 sheet: -0.25 (0.31), residues: 267 loop : -1.85 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 216 HIS 0.009 0.001 HIS F 197 PHE 0.027 0.001 PHE B 118 TYR 0.027 0.001 TYR E 235 ARG 0.007 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 190 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: B 117 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6310 (ptm) REVERT: B 136 VAL cc_start: 0.7670 (OUTLIER) cc_final: 0.7404 (t) REVERT: C 79 SER cc_start: 0.7459 (p) cc_final: 0.7137 (p) REVERT: C 186 THR cc_start: 0.8013 (p) cc_final: 0.7743 (p) REVERT: C 193 MET cc_start: 0.7956 (mmm) cc_final: 0.7666 (mmm) REVERT: E 206 SER cc_start: 0.8005 (t) cc_final: 0.7792 (m) REVERT: F 238 ASN cc_start: 0.7871 (m-40) cc_final: 0.7515 (m110) REVERT: F 239 ASP cc_start: 0.6872 (t0) cc_final: 0.6564 (t0) REVERT: F 352 GLN cc_start: 0.7894 (mm110) cc_final: 0.7393 (mp10) outliers start: 37 outliers final: 22 residues processed: 210 average time/residue: 1.1622 time to fit residues: 260.2700 Evaluate side-chains 216 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 192 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 109 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 345 ASN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8912 Z= 0.178 Angle : 0.524 6.515 12095 Z= 0.275 Chirality : 0.043 0.192 1373 Planarity : 0.004 0.044 1537 Dihedral : 4.701 26.046 1224 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.13 % Allowed : 19.37 % Favored : 76.50 % 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 (0.24), residues: 1108 helix: -0.76 (0.29), residues: 351 sheet: -0.21 (0.31), residues: 269 loop : -1.69 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 68 HIS 0.010 0.001 HIS F 197 PHE 0.021 0.001 PHE B 118 TYR 0.025 0.001 TYR E 235 ARG 0.008 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 199 time to evaluate : 0.989 Fit side-chains REVERT: B 117 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6317 (ptm) REVERT: B 136 VAL cc_start: 0.7668 (OUTLIER) cc_final: 0.7401 (t) REVERT: B 217 TYR cc_start: 0.7783 (m-80) cc_final: 0.7417 (m-80) REVERT: C 186 THR cc_start: 0.7976 (p) cc_final: 0.7752 (p) REVERT: C 193 MET cc_start: 0.7935 (mmm) cc_final: 0.7674 (mmm) REVERT: C 222 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6434 (pmt) REVERT: C 326 THR cc_start: 0.7509 (p) cc_final: 0.7080 (t) REVERT: F 239 ASP cc_start: 0.6844 (t0) cc_final: 0.6558 (t0) REVERT: F 352 GLN cc_start: 0.7881 (mm110) cc_final: 0.7424 (mp10) outliers start: 38 outliers final: 22 residues processed: 218 average time/residue: 1.1662 time to fit residues: 271.1773 Evaluate side-chains 217 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 192 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 103 optimal weight: 0.0070 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 109 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 HIS E 142 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8912 Z= 0.178 Angle : 0.526 7.235 12095 Z= 0.276 Chirality : 0.043 0.190 1373 Planarity : 0.004 0.043 1537 Dihedral : 4.628 24.198 1224 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.68 % Allowed : 19.59 % Favored : 75.73 % 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: -1.42 (0.24), residues: 1108 helix: -0.59 (0.29), residues: 350 sheet: -0.13 (0.31), residues: 269 loop : -1.60 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 174 HIS 0.008 0.001 HIS F 197 PHE 0.021 0.001 PHE F 240 TYR 0.025 0.001 TYR E 235 ARG 0.007 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 195 time to evaluate : 1.064 Fit side-chains REVERT: B 117 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6363 (ptm) REVERT: B 136 VAL cc_start: 0.7654 (OUTLIER) cc_final: 0.7395 (t) REVERT: C 186 THR cc_start: 0.7957 (p) cc_final: 0.7736 (p) REVERT: C 222 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6231 (pmt) REVERT: C 233 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6897 (m-30) REVERT: C 326 THR cc_start: 0.7557 (p) cc_final: 0.6942 (t) REVERT: C 332 VAL cc_start: 0.7794 (t) cc_final: 0.7568 (t) REVERT: F 239 ASP cc_start: 0.6858 (t0) cc_final: 0.6551 (t0) REVERT: F 352 GLN cc_start: 0.7870 (mm110) cc_final: 0.7437 (mp10) outliers start: 43 outliers final: 24 residues processed: 221 average time/residue: 1.1733 time to fit residues: 276.4872 Evaluate side-chains 213 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 117 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 233 ASP Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8912 Z= 0.307 Angle : 0.595 9.411 12095 Z= 0.309 Chirality : 0.045 0.220 1373 Planarity : 0.004 0.044 1537 Dihedral : 4.987 31.175 1224 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.33 % Allowed : 19.70 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.38 (0.25), residues: 1108 helix: -0.58 (0.28), residues: 354 sheet: -0.08 (0.31), residues: 269 loop : -1.60 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 216 HIS 0.013 0.002 HIS B 282 PHE 0.026 0.002 PHE B 284 TYR 0.028 0.002 TYR E 235 ARG 0.008 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 183 time to evaluate : 0.820 Fit side-chains REVERT: B 33 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.6695 (tm) REVERT: B 136 VAL cc_start: 0.7657 (OUTLIER) cc_final: 0.7409 (t) REVERT: C 222 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.6227 (pmt) REVERT: E 85 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8459 (mt) REVERT: F 239 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6555 (t0) REVERT: F 352 GLN cc_start: 0.7883 (mm110) cc_final: 0.7451 (mp10) outliers start: 49 outliers final: 23 residues processed: 205 average time/residue: 1.1343 time to fit residues: 249.0179 Evaluate side-chains 208 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 180 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN E 142 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8912 Z= 0.231 Angle : 0.566 8.927 12095 Z= 0.293 Chirality : 0.044 0.215 1373 Planarity : 0.004 0.043 1537 Dihedral : 4.818 27.203 1224 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.03 % Allowed : 21.22 % Favored : 74.76 % 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: -1.24 (0.25), residues: 1108 helix: -0.43 (0.29), residues: 354 sheet: -0.07 (0.31), residues: 269 loop : -1.50 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 216 HIS 0.010 0.002 HIS B 282 PHE 0.022 0.002 PHE B 284 TYR 0.029 0.002 TYR E 235 ARG 0.008 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 1.030 Fit side-chains REVERT: B 33 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6582 (tm) REVERT: B 136 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7404 (t) REVERT: C 222 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6207 (pmt) REVERT: C 326 THR cc_start: 0.7534 (p) cc_final: 0.6768 (t) REVERT: E 85 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8456 (mt) REVERT: F 239 ASP cc_start: 0.6853 (t0) cc_final: 0.6573 (t0) REVERT: F 352 GLN cc_start: 0.7864 (mm110) cc_final: 0.7488 (mp10) outliers start: 37 outliers final: 24 residues processed: 204 average time/residue: 1.1351 time to fit residues: 247.3349 Evaluate side-chains 216 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain G residue 20 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.0170 chunk 90 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8912 Z= 0.191 Angle : 0.559 10.751 12095 Z= 0.287 Chirality : 0.043 0.207 1373 Planarity : 0.004 0.044 1537 Dihedral : 4.668 24.587 1224 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.92 % Allowed : 22.20 % Favored : 73.88 % 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: -1.13 (0.25), residues: 1108 helix: -0.28 (0.29), residues: 352 sheet: -0.09 (0.31), residues: 269 loop : -1.41 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 104 HIS 0.009 0.001 HIS B 282 PHE 0.019 0.001 PHE B 284 TYR 0.029 0.001 TYR E 235 ARG 0.008 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 188 time to evaluate : 1.163 Fit side-chains REVERT: B 33 LEU cc_start: 0.6770 (OUTLIER) cc_final: 0.6541 (tm) REVERT: B 136 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7405 (t) REVERT: C 222 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6238 (pmt) REVERT: C 326 THR cc_start: 0.7504 (p) cc_final: 0.6715 (t) REVERT: F 238 ASN cc_start: 0.7803 (m-40) cc_final: 0.7583 (m110) REVERT: F 239 ASP cc_start: 0.6821 (t0) cc_final: 0.6530 (t0) REVERT: F 352 GLN cc_start: 0.7851 (mm110) cc_final: 0.7478 (mp10) outliers start: 36 outliers final: 22 residues processed: 205 average time/residue: 1.1337 time to fit residues: 249.3824 Evaluate side-chains 209 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 184 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 18 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 0.0570 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8912 Z= 0.212 Angle : 0.567 9.941 12095 Z= 0.291 Chirality : 0.044 0.217 1373 Planarity : 0.004 0.045 1537 Dihedral : 4.678 24.735 1224 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.48 % Allowed : 22.85 % Favored : 73.67 % 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: -1.07 (0.25), residues: 1108 helix: -0.16 (0.29), residues: 352 sheet: -0.09 (0.31), residues: 269 loop : -1.42 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 211 HIS 0.008 0.001 HIS B 282 PHE 0.028 0.002 PHE F 240 TYR 0.028 0.001 TYR E 235 ARG 0.008 0.001 ARG F 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 0.963 Fit side-chains REVERT: B 33 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6558 (tm) REVERT: B 136 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7417 (t) REVERT: C 222 MET cc_start: 0.7410 (OUTLIER) cc_final: 0.6245 (pmt) REVERT: C 326 THR cc_start: 0.7534 (p) cc_final: 0.6704 (t) REVERT: F 238 ASN cc_start: 0.7854 (m-40) cc_final: 0.7627 (m110) REVERT: F 239 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6578 (t0) REVERT: F 352 GLN cc_start: 0.7855 (mm110) cc_final: 0.7460 (mp10) outliers start: 32 outliers final: 24 residues processed: 203 average time/residue: 1.2147 time to fit residues: 262.2913 Evaluate side-chains 215 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 187 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 105 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 147 HIS Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 222 MET Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 18 MET Chi-restraints excluded: chain F residue 184 ILE Chi-restraints excluded: chain F residue 239 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 36 optimal weight: 0.0030 chunk 90 optimal weight: 0.0050 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 77 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.3604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN E 142 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.151542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.136626 restraints weight = 11419.727| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.77 r_work: 0.3756 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8912 Z= 0.164 Angle : 0.550 9.496 12095 Z= 0.281 Chirality : 0.043 0.198 1373 Planarity : 0.004 0.045 1537 Dihedral : 4.491 21.393 1224 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.59 % Allowed : 22.52 % Favored : 73.88 % 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: -0.87 (0.25), residues: 1108 helix: 0.07 (0.29), residues: 352 sheet: 0.02 (0.31), residues: 266 loop : -1.34 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 211 HIS 0.008 0.001 HIS F 197 PHE 0.027 0.001 PHE F 240 TYR 0.027 0.001 TYR E 235 ARG 0.008 0.000 ARG F 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4462.61 seconds wall clock time: 79 minutes 24.37 seconds (4764.37 seconds total)