Starting phenix.real_space_refine on Fri Dec 8 16:05:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/12_2023/7xwo_33497.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/12_2023/7xwo_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_33497/12_2023/7xwo_33497.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/12_2023/7xwo_33497.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/12_2023/7xwo_33497.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xwo_33497/12_2023/7xwo_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-1.21rc1-5172/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: 5.01, per 1000 atoms: 0.57 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 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: 0.95 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: 2.47 Time building geometry restraints manager: 3.42 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: 1.090 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: 5.880 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.810 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.540 ------------------------------------------------------------------------------- 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 : 0.931 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 215 average time/residue: 1.0394 time to fit residues: 240.0418 Evaluate side-chains 190 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 189 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.3580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.8980 chunk 84 optimal weight: 0.0170 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 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: 0.0060 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.4634 ------------------------------------------------------------------------------- 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: 0.7118 moved from start: 0.1467 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= 0.188 Angle : 0.560 6.683 12095 Z= 0.299 Chirality : 0.042 0.208 1373 Planarity : 0.005 0.054 1537 Dihedral : 5.462 33.593 1223 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.05 % Allowed : 13.93 % Favored : 83.03 % 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: -3.28 (0.22), residues: 1108 helix: -3.07 (0.20), residues: 347 sheet: -0.76 (0.30), residues: 279 loop : -2.24 (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 0.037 0.001 PHE B 118 TYR 0.028 0.001 TYR E 235 ARG 0.004 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 226 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 6 residues processed: 209 average time/residue: 1.2260 time to fit residues: 272.9629 Evaluate side-chains 194 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 0.789 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1285 time to fit residues: 1.7512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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: 0.7107 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8912 Z= 0.181 Angle : 0.539 10.297 12095 Z= 0.283 Chirality : 0.043 0.193 1373 Planarity : 0.004 0.049 1537 Dihedral : 5.005 30.699 1223 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.81 % Allowed : 16.43 % Favored : 79.76 % 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: -2.35 (0.23), residues: 1108 helix: -1.81 (0.25), residues: 352 sheet: -0.40 (0.30), residues: 280 loop : -1.98 (0.25), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 56 HIS 0.007 0.001 HIS F 329 PHE 0.030 0.001 PHE B 118 TYR 0.025 0.001 TYR E 235 ARG 0.006 0.000 ARG F 35 *********************** 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 222 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 187 time to evaluate : 0.977 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 14 residues processed: 205 average time/residue: 1.1531 time to fit residues: 252.3169 Evaluate side-chains 194 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 1.1548 time to fit residues: 8.5935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 ASN B 109 GLN ** B 110 ASN ** 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: 0.7145 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8912 Z= 0.285 Angle : 0.583 7.551 12095 Z= 0.303 Chirality : 0.045 0.231 1373 Planarity : 0.004 0.048 1537 Dihedral : 5.151 32.861 1223 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.13 % Allowed : 17.85 % Favored : 78.02 % 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: -2.01 (0.24), residues: 1108 helix: -1.30 (0.27), residues: 359 sheet: -0.33 (0.31), residues: 269 loop : -1.87 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 216 HIS 0.009 0.001 HIS F 197 PHE 0.029 0.002 PHE B 118 TYR 0.030 0.002 TYR E 235 ARG 0.007 0.001 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 229 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 191 time to evaluate : 0.990 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 211 average time/residue: 1.1560 time to fit residues: 260.2879 Evaluate side-chains 205 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 185 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 7 average time/residue: 0.7170 time to fit residues: 6.8979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 74 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.2980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 246 ASN F 259 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2251 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= 0.183 Angle : 0.534 6.677 12095 Z= 0.280 Chirality : 0.043 0.199 1373 Planarity : 0.004 0.044 1537 Dihedral : 4.744 27.405 1223 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.59 % Allowed : 19.48 % Favored : 76.93 % 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: -1.63 (0.24), residues: 1108 helix: -0.87 (0.28), residues: 352 sheet: -0.15 (0.31), residues: 267 loop : -1.72 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 216 HIS 0.010 0.001 HIS F 197 PHE 0.021 0.001 PHE B 118 TYR 0.026 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 223 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 190 time to evaluate : 0.897 Fit side-chains outliers start: 33 outliers final: 20 residues processed: 210 average time/residue: 1.1518 time to fit residues: 258.2120 Evaluate side-chains 201 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 181 time to evaluate : 0.958 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 6 average time/residue: 1.1166 time to fit residues: 8.5669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8912 Z= 0.257 Angle : 0.560 7.809 12095 Z= 0.293 Chirality : 0.045 0.221 1373 Planarity : 0.004 0.044 1537 Dihedral : 4.904 30.854 1223 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.68 % Allowed : 19.48 % Favored : 75.84 % 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: -1.54 (0.24), residues: 1108 helix: -0.77 (0.28), residues: 353 sheet: -0.16 (0.31), residues: 269 loop : -1.64 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 216 HIS 0.009 0.001 HIS F 197 PHE 0.022 0.002 PHE B 118 TYR 0.028 0.002 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 231 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 0.891 Fit side-chains outliers start: 43 outliers final: 23 residues processed: 214 average time/residue: 1.1933 time to fit residues: 272.6798 Evaluate side-chains 205 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 5 average time/residue: 0.4001 time to fit residues: 3.6768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 65 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8912 Z= 0.199 Angle : 0.555 10.365 12095 Z= 0.285 Chirality : 0.043 0.206 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.708 26.442 1223 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.13 % Allowed : 20.46 % Favored : 75.41 % 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: -0.62 (0.28), residues: 350 sheet: -0.10 (0.31), residues: 267 loop : -1.59 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 211 HIS 0.009 0.001 HIS F 197 PHE 0.024 0.001 PHE B 284 TYR 0.027 0.001 TYR E 235 ARG 0.008 0.000 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 227 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 0.952 Fit side-chains outliers start: 38 outliers final: 25 residues processed: 213 average time/residue: 1.1663 time to fit residues: 266.0246 Evaluate side-chains 211 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 186 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 7 average time/residue: 0.6438 time to fit residues: 6.2822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.0070 chunk 9 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 246 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8912 Z= 0.207 Angle : 0.559 9.837 12095 Z= 0.287 Chirality : 0.043 0.202 1373 Planarity : 0.004 0.042 1537 Dihedral : 4.676 27.472 1223 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.57 % Allowed : 20.35 % Favored : 75.08 % 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: -1.27 (0.25), residues: 1108 helix: -0.41 (0.28), residues: 352 sheet: -0.14 (0.31), residues: 269 loop : -1.50 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 216 HIS 0.007 0.001 HIS F 197 PHE 0.021 0.002 PHE B 284 TYR 0.027 0.001 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 233 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 191 time to evaluate : 0.998 Fit side-chains outliers start: 42 outliers final: 26 residues processed: 216 average time/residue: 1.1529 time to fit residues: 266.0349 Evaluate side-chains 212 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 18 residues processed: 8 average time/residue: 0.7908 time to fit residues: 8.2198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 0.0570 chunk 64 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 282 HIS E 142 GLN ** F 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 246 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8912 Z= 0.242 Angle : 0.575 9.664 12095 Z= 0.296 Chirality : 0.044 0.214 1373 Planarity : 0.004 0.047 1537 Dihedral : 4.757 27.738 1223 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.70 % Allowed : 21.33 % Favored : 74.97 % 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: -1.23 (0.25), residues: 1108 helix: -0.38 (0.28), residues: 352 sheet: -0.17 (0.31), residues: 261 loop : -1.43 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 216 HIS 0.008 0.001 HIS F 197 PHE 0.026 0.002 PHE F 240 TYR 0.028 0.002 TYR E 235 ARG 0.008 0.001 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 219 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 185 time to evaluate : 0.895 Fit side-chains outliers start: 34 outliers final: 25 residues processed: 209 average time/residue: 1.1563 time to fit residues: 260.3486 Evaluate side-chains 208 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.021 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 17 residues processed: 8 average time/residue: 0.8486 time to fit residues: 8.6647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 68 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8912 Z= 0.220 Angle : 0.574 9.883 12095 Z= 0.294 Chirality : 0.044 0.203 1373 Planarity : 0.004 0.046 1537 Dihedral : 4.684 26.398 1223 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.83 % Allowed : 22.42 % 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: -1.11 (0.25), residues: 1108 helix: -0.27 (0.29), residues: 352 sheet: -0.11 (0.32), residues: 261 loop : -1.36 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 68 HIS 0.009 0.001 HIS F 329 PHE 0.026 0.002 PHE F 240 TYR 0.027 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 208 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 182 time to evaluate : 0.874 Fit side-chains outliers start: 26 outliers final: 23 residues processed: 205 average time/residue: 1.1925 time to fit residues: 261.1138 Evaluate side-chains 200 residues out of total 963 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 177 time to evaluate : 0.932 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 4 average time/residue: 0.5955 time to fit residues: 4.1015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0000 chunk 24 optimal weight: 0.7980 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 11 optimal weight: 0.0170 chunk 16 optimal weight: 0.0770 chunk 77 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.1638 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.152942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.138031 restraints weight = 11466.435| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 1.77 r_work: 0.3779 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8912 Z= 0.132 Angle : 0.550 9.583 12095 Z= 0.277 Chirality : 0.042 0.198 1373 Planarity : 0.004 0.043 1537 Dihedral : 4.267 20.057 1223 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.37 % Allowed : 22.09 % Favored : 74.54 % 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: -0.86 (0.25), residues: 1108 helix: -0.02 (0.29), residues: 354 sheet: 0.01 (0.31), residues: 277 loop : -1.28 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 68 HIS 0.007 0.001 HIS F 329 PHE 0.023 0.001 PHE F 240 TYR 0.021 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: 4483.59 seconds wall clock time: 79 minutes 59.05 seconds (4799.05 seconds total)