Starting phenix.real_space_refine on Mon Mar 11 14:20:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xat_33098/03_2024/7xat_33098.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xat_33098/03_2024/7xat_33098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xat_33098/03_2024/7xat_33098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xat_33098/03_2024/7xat_33098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xat_33098/03_2024/7xat_33098.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xat_33098/03_2024/7xat_33098.pdb" } resolution = 2.85 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= 0.002 sd= 0.132 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 54 5.16 5 C 5356 2.51 5 N 1447 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C GLU 12": "OE1" <-> "OE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 26": "OD1" <-> "OD2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 201": "OD1" <-> "OD2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8470 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 1929 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 11, 'TRANS': 274} Unresolved non-hydrogen bonds: 355 Unresolved non-hydrogen angles: 443 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 10, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 188 Chain: "B" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1591 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 1, 'GLU:plan': 11, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 130 Chain: "C" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "F" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 92 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 5.02, per 1000 atoms: 0.59 Number of scatterers: 8470 At special positions: 0 Unit cell: (87.74, 120.91, 125.19, 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 54 16.00 O 1613 8.00 N 1447 7.00 C 5356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.06 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.04 Simple disulfide: pdb=" SG CYS F 3 " - pdb=" SG CYS F 14 " distance=2.04 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: 3.37 Conformation dependent library (CDL) restraints added in 1.6 seconds 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2154 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 30.3% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 41 through 71 removed outlier: 3.961A pdb=" N VAL A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.526A pdb=" N ALA A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 removed outlier: 4.196A pdb=" N GLN A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 120 through 125 removed outlier: 3.644A pdb=" N ASN A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 145 removed outlier: 3.579A pdb=" N VAL A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 180 removed outlier: 3.514A pdb=" N MET A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 171 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 201 through 205 removed outlier: 3.570A pdb=" N TYR A 205 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 Processing helix chain 'A' and resid 217 through 239 removed outlier: 4.171A pdb=" N LEU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.558A pdb=" N PHE A 265 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 266 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.544A pdb=" N PHE A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 301 removed outlier: 3.927A pdb=" N ASP A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.653A pdb=" N GLU B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET B 18 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 22 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 52 removed outlier: 3.688A pdb=" N ILE B 49 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.563A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.637A pdb=" N ASP B 229 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 230 " --> pdb=" O LEU B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 243 through 255 removed outlier: 3.790A pdb=" N LEU B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 251 " --> pdb=" O MET B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 279 removed outlier: 3.732A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LYS B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 4.065A pdb=" N ALA B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.583A pdb=" N PHE B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 349 " --> pdb=" O LYS B 345 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 351 " --> pdb=" O ASN B 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 25 removed outlier: 3.636A pdb=" N ILE C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA C 21 " --> pdb=" O GLN C 17 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 7 through 25 removed outlier: 3.584A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA D 23 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 35 Processing helix chain 'D' and resid 38 through 44 removed outlier: 3.552A pdb=" N GLU D 42 " --> pdb=" O MET D 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 188 removed outlier: 6.103A pdb=" N VAL B 34 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N PHE B 199 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU B 36 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 52 removed outlier: 5.713A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.589A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 3.901A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.944A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.924A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.465A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.843A pdb=" N ASP C 303 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.533A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.601A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.547A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 299 hydrogen bonds defined for protein. 834 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: 2.49 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2704 1.34 - 1.47: 2215 1.47 - 1.60: 3636 1.60 - 1.73: 0 1.73 - 1.86: 74 Bond restraints: 8629 Sorted by residual: bond pdb=" CG1 ILE C 273 " pdb=" CD1 ILE C 273 " ideal model delta sigma weight residual 1.513 1.403 0.110 3.90e-02 6.57e+02 7.97e+00 bond pdb=" CG LEU C 146 " pdb=" CD2 LEU C 146 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.28e+00 bond pdb=" CG1 ILE C 58 " pdb=" CD1 ILE C 58 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.25e+00 bond pdb=" CG1 ILE C 338 " pdb=" CD1 ILE C 338 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.23e+00 bond pdb=" CA SER B 16 " pdb=" CB SER B 16 " ideal model delta sigma weight residual 1.529 1.489 0.040 1.74e-02 3.30e+03 5.29e+00 ... (remaining 8624 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.75: 146 105.75 - 112.84: 4552 112.84 - 119.93: 3068 119.93 - 127.02: 3883 127.02 - 134.11: 98 Bond angle restraints: 11747 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 angle pdb=" C ASP C 291 " pdb=" N PHE C 292 " pdb=" CA PHE C 292 " ideal model delta sigma weight residual 121.54 129.49 -7.95 1.91e+00 2.74e-01 1.73e+01 angle pdb=" C PHE F 11 " pdb=" N THR F 12 " pdb=" CA THR F 12 " ideal model delta sigma weight residual 120.82 126.62 -5.80 1.41e+00 5.03e-01 1.69e+01 angle pdb=" N ARG A 157 " pdb=" CA ARG A 157 " pdb=" C ARG A 157 " ideal model delta sigma weight residual 113.18 108.11 5.07 1.33e+00 5.65e-01 1.45e+01 angle pdb=" N LYS B 314 " pdb=" CA LYS B 314 " pdb=" C LYS B 314 " ideal model delta sigma weight residual 112.38 117.01 -4.63 1.22e+00 6.72e-01 1.44e+01 ... (remaining 11742 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 4580 16.65 - 33.29: 425 33.29 - 49.94: 78 49.94 - 66.58: 11 66.58 - 83.23: 7 Dihedral angle restraints: 5101 sinusoidal: 1767 harmonic: 3334 Sorted by residual: dihedral pdb=" CB CYS C 121 " pdb=" SG CYS C 121 " pdb=" SG CYS C 149 " pdb=" CB CYS C 149 " ideal model delta sinusoidal sigma weight residual 93.00 167.02 -74.02 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA LEU A 270 " pdb=" C LEU A 270 " pdb=" N PRO A 271 " pdb=" CA PRO A 271 " ideal model delta harmonic sigma weight residual 180.00 138.73 41.27 0 5.00e+00 4.00e-02 6.81e+01 dihedral pdb=" CA THR A 206 " pdb=" C THR A 206 " pdb=" N GLY A 207 " pdb=" CA GLY A 207 " ideal model delta harmonic sigma weight residual -180.00 -152.68 -27.32 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 5098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1130 0.073 - 0.146: 232 0.146 - 0.219: 24 0.219 - 0.292: 3 0.292 - 0.365: 1 Chirality restraints: 1390 Sorted by residual: chirality pdb=" CG LEU E 174 " pdb=" CB LEU E 174 " pdb=" CD1 LEU E 174 " pdb=" CD2 LEU E 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CB THR D 52 " pdb=" CA THR D 52 " pdb=" OG1 THR D 52 " pdb=" CG2 THR D 52 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1387 not shown) Planarity restraints: 1500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " -0.057 5.00e-02 4.00e+02 8.56e-02 1.17e+01 pdb=" N PRO A 271 " 0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 175 " 0.050 5.00e-02 4.00e+02 7.45e-02 8.89e+00 pdb=" N PRO A 176 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 176 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 176 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO E 75 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " -0.037 5.00e-02 4.00e+02 ... (remaining 1497 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1360 2.75 - 3.29: 7467 3.29 - 3.83: 14136 3.83 - 4.36: 17291 4.36 - 4.90: 29825 Nonbonded interactions: 70079 Sorted by model distance: nonbonded pdb=" O ILE A 209 " pdb=" OH TYR A 273 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.245 2.440 nonbonded pdb=" O HIS A 146 " pdb=" OG SER A 150 " model vdw 2.282 2.440 nonbonded pdb=" O ASN A 43 " pdb=" OG1 THR A 47 " model vdw 2.283 2.440 nonbonded pdb=" O SER B 228 " pdb=" OG SER B 228 " model vdw 2.302 2.440 ... (remaining 70074 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: 0.830 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: 2.220 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.880 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.010 0.110 8629 Z= 0.625 Angle : 1.000 11.109 11747 Z= 0.557 Chirality : 0.060 0.365 1390 Planarity : 0.007 0.086 1500 Dihedral : 13.720 83.226 2935 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 0.82 % Allowed : 8.06 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -4.15 (0.21), residues: 1137 helix: -4.60 (0.13), residues: 332 sheet: -1.16 (0.29), residues: 294 loop : -2.27 (0.23), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP C 63 HIS 0.006 0.002 HIS E 167 PHE 0.034 0.003 PHE B 189 TYR 0.021 0.003 TYR A 273 ARG 0.010 0.001 ARG C 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 189 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 PHE cc_start: 0.8564 (m-10) cc_final: 0.8152 (m-10) REVERT: A 160 LYS cc_start: 0.7872 (mttp) cc_final: 0.7085 (mmtt) REVERT: A 272 PHE cc_start: 0.8492 (t80) cc_final: 0.8097 (t80) REVERT: A 294 PHE cc_start: 0.8229 (t80) cc_final: 0.8023 (t80) REVERT: A 302 TYR cc_start: 0.8608 (m-80) cc_final: 0.8321 (m-80) REVERT: B 341 ASP cc_start: 0.8091 (t70) cc_final: 0.7888 (t0) REVERT: C 258 ASP cc_start: 0.7338 (t0) cc_final: 0.7080 (t70) REVERT: E 46 GLU cc_start: 0.7975 (pt0) cc_final: 0.7600 (pt0) REVERT: E 51 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8137 (tt) REVERT: F 7 PHE cc_start: 0.7875 (t80) cc_final: 0.7608 (t80) outliers start: 7 outliers final: 3 residues processed: 194 average time/residue: 1.1347 time to fit residues: 234.2803 Evaluate side-chains 159 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 8.9990 chunk 34 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 146 HIS B 188 HIS B 255 ASN B 346 ASN C 62 HIS C 237 ASN ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 ASN E 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8629 Z= 0.186 Angle : 0.597 7.362 11747 Z= 0.320 Chirality : 0.042 0.136 1390 Planarity : 0.005 0.071 1500 Dihedral : 6.080 55.391 1235 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.99 % Allowed : 15.19 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -3.22 (0.22), residues: 1137 helix: -3.41 (0.19), residues: 354 sheet: -0.84 (0.28), residues: 296 loop : -1.78 (0.26), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 339 HIS 0.003 0.001 HIS C 91 PHE 0.014 0.001 PHE B 189 TYR 0.012 0.001 TYR A 50 ARG 0.005 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.054 Fit side-chains REVERT: A 56 ILE cc_start: 0.7930 (tp) cc_final: 0.7649 (pt) REVERT: A 131 PHE cc_start: 0.8479 (m-10) cc_final: 0.8076 (m-10) REVERT: A 160 LYS cc_start: 0.7132 (mttp) cc_final: 0.6406 (mmtt) REVERT: A 272 PHE cc_start: 0.8346 (t80) cc_final: 0.8135 (t80) REVERT: B 35 LYS cc_start: 0.8307 (mtmm) cc_final: 0.7833 (mtmt) REVERT: B 341 ASP cc_start: 0.7840 (t70) cc_final: 0.7634 (t0) REVERT: C 258 ASP cc_start: 0.7128 (t0) cc_final: 0.6917 (t70) REVERT: E 46 GLU cc_start: 0.7926 (pt0) cc_final: 0.7526 (pt0) REVERT: E 89 GLU cc_start: 0.7667 (mp0) cc_final: 0.7257 (pm20) REVERT: E 201 ASP cc_start: 0.7580 (t0) cc_final: 0.7297 (t0) REVERT: E 218 ARG cc_start: 0.6882 (ptp90) cc_final: 0.6548 (ptp-170) outliers start: 17 outliers final: 8 residues processed: 180 average time/residue: 1.0541 time to fit residues: 203.3322 Evaluate side-chains 162 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 154 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 303 ASP Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8629 Z= 0.269 Angle : 0.613 8.642 11747 Z= 0.322 Chirality : 0.043 0.135 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.793 58.612 1229 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.86 % Allowed : 16.82 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.66 (0.23), residues: 1137 helix: -2.67 (0.22), residues: 358 sheet: -0.57 (0.28), residues: 300 loop : -1.65 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.004 0.001 HIS C 91 PHE 0.013 0.001 PHE B 189 TYR 0.014 0.001 TYR A 273 ARG 0.005 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 1.056 Fit side-chains REVERT: A 56 ILE cc_start: 0.7959 (tp) cc_final: 0.7653 (pt) REVERT: A 114 ILE cc_start: 0.7090 (mp) cc_final: 0.6844 (OUTLIER) REVERT: A 131 PHE cc_start: 0.8445 (m-10) cc_final: 0.8133 (m-10) REVERT: A 160 LYS cc_start: 0.7227 (mttp) cc_final: 0.6384 (mmtt) REVERT: A 272 PHE cc_start: 0.8351 (t80) cc_final: 0.8127 (t80) REVERT: A 302 TYR cc_start: 0.8551 (m-80) cc_final: 0.8343 (m-80) REVERT: B 341 ASP cc_start: 0.7879 (t70) cc_final: 0.7652 (t0) REVERT: C 129 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6573 (tpt-90) REVERT: C 212 ASP cc_start: 0.8079 (t70) cc_final: 0.7710 (t0) REVERT: C 214 ARG cc_start: 0.7804 (mmm-85) cc_final: 0.7528 (mmm-85) REVERT: C 247 ASP cc_start: 0.7776 (t0) cc_final: 0.7519 (t0) REVERT: E 46 GLU cc_start: 0.7934 (pt0) cc_final: 0.7558 (pt0) REVERT: E 89 GLU cc_start: 0.7681 (mp0) cc_final: 0.7264 (pm20) REVERT: E 201 ASP cc_start: 0.7746 (t0) cc_final: 0.7408 (t0) outliers start: 33 outliers final: 15 residues processed: 169 average time/residue: 1.1154 time to fit residues: 201.4014 Evaluate side-chains 167 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 237 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8629 Z= 0.179 Angle : 0.553 7.326 11747 Z= 0.291 Chirality : 0.041 0.132 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.378 58.609 1229 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 3.86 % Allowed : 17.87 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -2.11 (0.24), residues: 1137 helix: -2.03 (0.25), residues: 352 sheet: -0.32 (0.29), residues: 290 loop : -1.44 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.012 0.001 TYR A 273 ARG 0.004 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.016 Fit side-chains REVERT: A 56 ILE cc_start: 0.8015 (tp) cc_final: 0.7691 (pt) REVERT: A 114 ILE cc_start: 0.7271 (mp) cc_final: 0.7033 (OUTLIER) REVERT: A 131 PHE cc_start: 0.8485 (m-10) cc_final: 0.8202 (m-10) REVERT: A 160 LYS cc_start: 0.7169 (mttp) cc_final: 0.6317 (mmtt) REVERT: A 272 PHE cc_start: 0.8328 (t80) cc_final: 0.8050 (t80) REVERT: A 302 TYR cc_start: 0.8550 (m-80) cc_final: 0.8326 (m-80) REVERT: B 35 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7818 (mtmt) REVERT: B 184 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8630 (tp) REVERT: B 274 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.6460 (t80) REVERT: B 341 ASP cc_start: 0.7857 (t70) cc_final: 0.7533 (t0) REVERT: C 96 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.6568 (mtt-85) REVERT: C 129 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.6539 (tpt-90) REVERT: C 212 ASP cc_start: 0.8064 (t70) cc_final: 0.7735 (t0) REVERT: C 214 ARG cc_start: 0.7762 (mmm-85) cc_final: 0.7520 (mmm-85) REVERT: C 258 ASP cc_start: 0.6838 (t70) cc_final: 0.5958 (t70) REVERT: E 46 GLU cc_start: 0.7887 (pt0) cc_final: 0.7516 (pt0) REVERT: E 89 GLU cc_start: 0.7619 (mp0) cc_final: 0.7165 (pm20) REVERT: E 109 ASP cc_start: 0.7797 (p0) cc_final: 0.7587 (p0) outliers start: 33 outliers final: 18 residues processed: 187 average time/residue: 1.0092 time to fit residues: 202.9848 Evaluate side-chains 169 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8629 Z= 0.222 Angle : 0.570 7.793 11747 Z= 0.297 Chirality : 0.042 0.147 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.303 56.824 1229 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.44 % Allowed : 19.63 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.76 (0.24), residues: 1137 helix: -1.62 (0.26), residues: 355 sheet: -0.21 (0.29), residues: 295 loop : -1.27 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.015 0.001 TYR A 273 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 148 time to evaluate : 1.128 Fit side-chains REVERT: A 131 PHE cc_start: 0.8473 (m-10) cc_final: 0.8194 (m-10) REVERT: A 160 LYS cc_start: 0.7220 (mttp) cc_final: 0.6346 (mmtt) REVERT: A 246 LYS cc_start: 0.6755 (ptpt) cc_final: 0.6503 (ttpm) REVERT: A 272 PHE cc_start: 0.8346 (t80) cc_final: 0.8020 (t80) REVERT: A 302 TYR cc_start: 0.8554 (m-80) cc_final: 0.8344 (m-80) REVERT: B 35 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7818 (mtmt) REVERT: B 184 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8685 (tp) REVERT: B 274 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6525 (t80) REVERT: B 341 ASP cc_start: 0.7833 (t70) cc_final: 0.7625 (t0) REVERT: C 96 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6678 (mtt-85) REVERT: C 129 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6545 (tpt-90) REVERT: C 212 ASP cc_start: 0.8057 (t70) cc_final: 0.7756 (t0) REVERT: C 214 ARG cc_start: 0.7713 (mmm-85) cc_final: 0.7506 (mmm-85) REVERT: C 258 ASP cc_start: 0.6806 (t70) cc_final: 0.5862 (t70) REVERT: E 46 GLU cc_start: 0.7873 (pt0) cc_final: 0.7543 (pt0) REVERT: E 89 GLU cc_start: 0.7566 (mp0) cc_final: 0.7175 (pm20) REVERT: E 109 ASP cc_start: 0.7828 (p0) cc_final: 0.7610 (p0) REVERT: E 218 ARG cc_start: 0.6539 (ptp90) cc_final: 0.6255 (mtm-85) outliers start: 38 outliers final: 22 residues processed: 171 average time/residue: 1.0414 time to fit residues: 190.9563 Evaluate side-chains 172 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8629 Z= 0.251 Angle : 0.582 8.436 11747 Z= 0.301 Chirality : 0.043 0.134 1390 Planarity : 0.004 0.070 1500 Dihedral : 5.293 55.212 1229 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.32 % Allowed : 20.33 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.61 (0.24), residues: 1137 helix: -1.42 (0.27), residues: 359 sheet: -0.15 (0.29), residues: 295 loop : -1.22 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 63 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.015 0.001 TYR A 273 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 157 time to evaluate : 0.900 Fit side-chains REVERT: A 56 ILE cc_start: 0.8000 (tp) cc_final: 0.7673 (pt) REVERT: A 131 PHE cc_start: 0.8434 (m-10) cc_final: 0.8185 (m-10) REVERT: A 160 LYS cc_start: 0.7217 (mttp) cc_final: 0.6351 (mmtt) REVERT: A 272 PHE cc_start: 0.8368 (t80) cc_final: 0.8011 (t80) REVERT: A 302 TYR cc_start: 0.8542 (m-80) cc_final: 0.8328 (m-80) REVERT: B 35 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7833 (mtmt) REVERT: B 184 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8816 (tp) REVERT: B 274 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6679 (t80) REVERT: B 341 ASP cc_start: 0.7833 (t70) cc_final: 0.7531 (t0) REVERT: C 96 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6662 (mtt-85) REVERT: C 129 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6567 (tpt-90) REVERT: C 212 ASP cc_start: 0.8054 (t70) cc_final: 0.7742 (t0) REVERT: C 258 ASP cc_start: 0.6741 (t70) cc_final: 0.5798 (t70) REVERT: E 46 GLU cc_start: 0.7856 (pt0) cc_final: 0.7496 (pt0) REVERT: E 89 GLU cc_start: 0.7589 (mp0) cc_final: 0.7197 (pm20) REVERT: E 109 ASP cc_start: 0.7846 (p0) cc_final: 0.7616 (p0) REVERT: E 218 ARG cc_start: 0.6526 (ptp90) cc_final: 0.6245 (mtm-85) outliers start: 37 outliers final: 26 residues processed: 179 average time/residue: 1.0875 time to fit residues: 208.1268 Evaluate side-chains 181 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 151 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 274 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8629 Z= 0.173 Angle : 0.545 8.183 11747 Z= 0.281 Chirality : 0.042 0.130 1390 Planarity : 0.004 0.069 1500 Dihedral : 5.035 53.830 1229 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 4.09 % Allowed : 21.50 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.40 (0.25), residues: 1137 helix: -1.16 (0.27), residues: 363 sheet: -0.07 (0.30), residues: 290 loop : -1.14 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.003 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.013 0.001 TYR A 273 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 1.047 Fit side-chains REVERT: A 114 ILE cc_start: 0.7272 (mp) cc_final: 0.7036 (mt) REVERT: A 131 PHE cc_start: 0.8440 (m-10) cc_final: 0.8213 (m-10) REVERT: A 160 LYS cc_start: 0.7233 (mttp) cc_final: 0.6345 (mmtt) REVERT: A 272 PHE cc_start: 0.8338 (t80) cc_final: 0.7907 (t80) REVERT: A 302 TYR cc_start: 0.8547 (m-80) cc_final: 0.8319 (m-80) REVERT: B 35 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7852 (mtmt) REVERT: B 184 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8774 (tp) REVERT: B 309 ASP cc_start: 0.7684 (m-30) cc_final: 0.7426 (p0) REVERT: B 341 ASP cc_start: 0.7800 (t70) cc_final: 0.7497 (t0) REVERT: C 96 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6686 (mtt-85) REVERT: C 129 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6491 (tpt-90) REVERT: C 212 ASP cc_start: 0.8016 (t70) cc_final: 0.7757 (t0) REVERT: C 258 ASP cc_start: 0.6617 (t70) cc_final: 0.5629 (t70) REVERT: E 46 GLU cc_start: 0.7829 (pt0) cc_final: 0.7478 (pt0) REVERT: E 89 GLU cc_start: 0.7515 (mp0) cc_final: 0.7131 (pm20) REVERT: E 109 ASP cc_start: 0.7705 (p0) cc_final: 0.7503 (p0) REVERT: E 218 ARG cc_start: 0.6448 (ptp90) cc_final: 0.6157 (mtm-85) outliers start: 35 outliers final: 24 residues processed: 176 average time/residue: 1.0375 time to fit residues: 196.2959 Evaluate side-chains 179 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 135 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8629 Z= 0.155 Angle : 0.535 8.056 11747 Z= 0.277 Chirality : 0.041 0.130 1390 Planarity : 0.004 0.069 1500 Dihedral : 4.648 38.058 1227 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.97 % Allowed : 22.08 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.19 (0.25), residues: 1137 helix: -0.96 (0.28), residues: 358 sheet: 0.06 (0.30), residues: 287 loop : -1.05 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 82 HIS 0.003 0.000 HIS C 91 PHE 0.012 0.001 PHE E 80 TYR 0.014 0.001 TYR B 296 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 153 time to evaluate : 1.053 Fit side-chains REVERT: A 131 PHE cc_start: 0.8438 (m-10) cc_final: 0.8224 (m-10) REVERT: A 160 LYS cc_start: 0.7228 (mttp) cc_final: 0.6328 (mmtt) REVERT: A 272 PHE cc_start: 0.8276 (t80) cc_final: 0.7906 (t80) REVERT: A 302 TYR cc_start: 0.8531 (m-80) cc_final: 0.8329 (m-80) REVERT: B 35 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7832 (mtmt) REVERT: B 184 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8744 (tp) REVERT: B 192 LYS cc_start: 0.7921 (mtpt) cc_final: 0.7622 (mtpp) REVERT: B 341 ASP cc_start: 0.7783 (t70) cc_final: 0.7488 (t0) REVERT: C 129 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6471 (tpt-90) REVERT: C 212 ASP cc_start: 0.7974 (t70) cc_final: 0.7762 (t0) REVERT: C 258 ASP cc_start: 0.6591 (t70) cc_final: 0.5525 (t70) REVERT: E 46 GLU cc_start: 0.7806 (pt0) cc_final: 0.7446 (pt0) REVERT: E 76 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7861 (ptpp) REVERT: E 89 GLU cc_start: 0.7545 (mp0) cc_final: 0.7135 (pm20) REVERT: E 109 ASP cc_start: 0.7739 (p0) cc_final: 0.7535 (p0) REVERT: E 218 ARG cc_start: 0.6493 (ptp90) cc_final: 0.6210 (mtm-85) outliers start: 34 outliers final: 25 residues processed: 177 average time/residue: 1.1360 time to fit residues: 216.8712 Evaluate side-chains 177 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 149 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 65 optimal weight: 0.0980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 255 ASN C 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8629 Z= 0.249 Angle : 0.590 8.267 11747 Z= 0.305 Chirality : 0.043 0.135 1390 Planarity : 0.004 0.070 1500 Dihedral : 4.816 37.108 1227 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.62 % Allowed : 22.66 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.21 (0.25), residues: 1137 helix: -0.98 (0.27), residues: 359 sheet: 0.07 (0.30), residues: 288 loop : -1.07 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.004 0.001 HIS C 91 PHE 0.012 0.001 PHE B 189 TYR 0.016 0.001 TYR A 273 ARG 0.009 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 1.014 Fit side-chains REVERT: A 302 TYR cc_start: 0.8533 (m-80) cc_final: 0.8307 (m-80) REVERT: B 35 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7857 (mtmt) REVERT: B 184 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8830 (tp) REVERT: B 309 ASP cc_start: 0.7606 (m-30) cc_final: 0.7208 (p0) REVERT: B 341 ASP cc_start: 0.7824 (t70) cc_final: 0.7512 (t0) REVERT: C 45 MET cc_start: 0.8816 (mtt) cc_final: 0.8347 (mtt) REVERT: C 96 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.6691 (mtt-85) REVERT: C 129 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6510 (tpt-90) REVERT: C 212 ASP cc_start: 0.8036 (t70) cc_final: 0.7772 (OUTLIER) REVERT: C 258 ASP cc_start: 0.6673 (t70) cc_final: 0.5582 (t70) REVERT: E 46 GLU cc_start: 0.7849 (pt0) cc_final: 0.7500 (pt0) REVERT: E 89 GLU cc_start: 0.7511 (mp0) cc_final: 0.7138 (pm20) REVERT: E 109 ASP cc_start: 0.7820 (p0) cc_final: 0.7607 (p0) REVERT: E 218 ARG cc_start: 0.6539 (ptp90) cc_final: 0.6261 (mtm-85) outliers start: 31 outliers final: 28 residues processed: 169 average time/residue: 1.0497 time to fit residues: 190.2361 Evaluate side-chains 176 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 243 MET Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 129 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Chi-restraints excluded: chain F residue 12 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.0670 chunk 74 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 95 optimal weight: 0.0030 chunk 27 optimal weight: 4.9990 overall best weight: 0.5130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8629 Z= 0.140 Angle : 0.535 8.509 11747 Z= 0.276 Chirality : 0.041 0.132 1390 Planarity : 0.004 0.069 1500 Dihedral : 4.551 37.721 1227 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.57 % Allowed : 23.83 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.05 (0.25), residues: 1137 helix: -0.77 (0.27), residues: 359 sheet: 0.08 (0.30), residues: 288 loop : -0.99 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 82 HIS 0.002 0.000 HIS C 91 PHE 0.019 0.001 PHE A 131 TYR 0.016 0.001 TYR B 296 ARG 0.007 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2274 Ramachandran restraints generated. 1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.078 Fit side-chains REVERT: A 131 PHE cc_start: 0.8583 (m-10) cc_final: 0.8291 (m-10) REVERT: B 35 LYS cc_start: 0.8291 (mtmm) cc_final: 0.7837 (mtmt) REVERT: B 184 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8741 (tp) REVERT: B 192 LYS cc_start: 0.7899 (mtpt) cc_final: 0.7601 (mtpp) REVERT: B 252 SER cc_start: 0.8556 (OUTLIER) cc_final: 0.8308 (p) REVERT: B 341 ASP cc_start: 0.7757 (t70) cc_final: 0.7450 (t0) REVERT: C 96 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6687 (mtt-85) REVERT: C 258 ASP cc_start: 0.6586 (t70) cc_final: 0.5538 (t70) REVERT: E 46 GLU cc_start: 0.7782 (pt0) cc_final: 0.7442 (pt0) REVERT: E 89 GLU cc_start: 0.7514 (mp0) cc_final: 0.7197 (pm20) REVERT: E 109 ASP cc_start: 0.7669 (p0) cc_final: 0.7466 (p0) outliers start: 22 outliers final: 19 residues processed: 173 average time/residue: 0.9992 time to fit residues: 185.9660 Evaluate side-chains 172 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 139 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 252 SER Chi-restraints excluded: chain B residue 261 ASP Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 226 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 64 optimal weight: 0.0570 overall best weight: 1.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 255 ASN C 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123913 restraints weight = 10053.268| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.17 r_work: 0.3255 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8629 Z= 0.302 Angle : 0.622 8.828 11747 Z= 0.322 Chirality : 0.045 0.160 1390 Planarity : 0.004 0.070 1500 Dihedral : 4.848 36.822 1227 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.15 % Allowed : 23.71 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: -1.04 (0.25), residues: 1137 helix: -0.75 (0.27), residues: 357 sheet: 0.06 (0.30), residues: 293 loop : -0.98 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 36 HIS 0.004 0.001 HIS C 91 PHE 0.013 0.002 PHE E 80 TYR 0.018 0.002 TYR A 273 ARG 0.004 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.16 seconds wall clock time: 68 minutes 42.41 seconds (4122.41 seconds total)