Starting phenix.real_space_refine on Wed Feb 14 05:19:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/02_2024/7y1f_33562.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/02_2024/7y1f_33562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/02_2024/7y1f_33562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/02_2024/7y1f_33562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/02_2024/7y1f_33562.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y1f_33562/02_2024/7y1f_33562.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 5561 2.51 5 N 1480 2.21 5 O 1590 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 7": "NH1" <-> "NH2" Residue "R TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 188": "NH1" <-> "NH2" Residue "R TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 272": "NH1" <-> "NH2" Residue "R ASP 325": "OD1" <-> "OD2" Residue "R PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 359": "NH1" <-> "NH2" Residue "R ASP 368": "OD1" <-> "OD2" Residue "R ARG 369": "NH1" <-> "NH2" Residue "R PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 436": "OD1" <-> "OD2" Residue "R PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 441": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ASP 27": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 247": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E ASP 125": "OD1" <-> "OD2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "E TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8691 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1679 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 46 Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 80 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "R" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2256 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Time building chain proxies: 4.87, per 1000 atoms: 0.56 Number of scatterers: 8691 At special positions: 0 Unit cell: (102.6, 112.32, 135, 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 1590 8.00 N 1480 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 233 " - pdb=" SG CYS R 312 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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: 3.10 Conformation dependent library (CDL) restraints added in 1.7 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 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: 25 helices and 14 sheets defined 35.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 11 through 32 Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.238A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 216 removed outlier: 3.575A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 244 through 254 removed outlier: 4.208A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 281 removed outlier: 3.571A pdb=" N SER A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.979A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.971A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 345 Processing helix chain 'R' and resid 159 through 189 Processing helix chain 'R' and resid 194 through 212 removed outlier: 3.768A pdb=" N ILE R 198 " --> pdb=" O THR R 194 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 223 removed outlier: 4.097A pdb=" N VAL R 220 " --> pdb=" O PHE R 216 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR R 221 " --> pdb=" O GLN R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 264 removed outlier: 3.568A pdb=" N HIS R 264 " --> pdb=" O ILE R 260 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 272 removed outlier: 4.019A pdb=" N LEU R 269 " --> pdb=" O PRO R 265 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP R 270 " --> pdb=" O VAL R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 298 removed outlier: 4.137A pdb=" N VAL R 291 " --> pdb=" O LEU R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 323 through 337 Processing helix chain 'R' and resid 337 through 357 removed outlier: 4.213A pdb=" N SER R 357 " --> pdb=" O LEU R 353 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 399 removed outlier: 3.782A pdb=" N ASP R 368 " --> pdb=" O SER R 364 " (cutoff:3.500A) Proline residue: R 391 - end of helix Processing helix chain 'R' and resid 409 through 433 removed outlier: 4.344A pdb=" N SER R 413 " --> pdb=" O ALA R 409 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER R 425 " --> pdb=" O GLY R 421 " (cutoff:3.500A) Proline residue: R 429 - end of helix Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.965A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 24 removed outlier: 3.859A pdb=" N GLU C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.615A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.519A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.545A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36 removed outlier: 6.392A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 226 removed outlier: 5.654A pdb=" N PHE A 223 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE A 267 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 299 through 302 removed outlier: 3.794A pdb=" N GLY R 300 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER R 313 " --> pdb=" O GLY R 300 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU R 311 " --> pdb=" O LYS R 302 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.696A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.167A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.470A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.690A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.700A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.777A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.137A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1131 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: 2.76 Time building geometry restraints manager: 3.40 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: 2767 1.34 - 1.47: 2247 1.47 - 1.59: 3770 1.59 - 1.72: 0 1.72 - 1.84: 87 Bond restraints: 8871 Sorted by residual: bond pdb=" C GLU E 222 " pdb=" N TYR E 223 " ideal model delta sigma weight residual 1.335 1.247 0.087 3.04e-02 1.08e+03 8.23e+00 bond pdb=" CG1 ILE B 273 " pdb=" CD1 ILE B 273 " ideal model delta sigma weight residual 1.513 1.414 0.099 3.90e-02 6.57e+02 6.49e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.731 0.077 3.30e-02 9.18e+02 5.45e+00 bond pdb=" CG1 ILE B 338 " pdb=" CD1 ILE B 338 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.29e+00 bond pdb=" CB VAL B 112 " pdb=" CG1 VAL B 112 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.16e+00 ... (remaining 8866 not shown) Histogram of bond angle deviations from ideal: 97.62 - 104.95: 126 104.95 - 112.27: 4398 112.27 - 119.60: 2954 119.60 - 126.93: 4430 126.93 - 134.25: 127 Bond angle restraints: 12035 Sorted by residual: angle pdb=" C GLU R 305 " pdb=" N ASP R 306 " pdb=" CA ASP R 306 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" CA LEU A 353 " pdb=" CB LEU A 353 " pdb=" CG LEU A 353 " ideal model delta sigma weight residual 116.30 133.18 -16.88 3.50e+00 8.16e-02 2.33e+01 angle pdb=" C ALA E 209 " pdb=" N GLU E 210 " pdb=" CA GLU E 210 " 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 B 247 " pdb=" N ALA B 248 " pdb=" CA ALA B 248 " ideal model delta sigma weight residual 122.74 128.70 -5.96 1.44e+00 4.82e-01 1.71e+01 angle pdb=" C ASP B 246 " pdb=" N ASP B 247 " pdb=" CA ASP B 247 " ideal model delta sigma weight residual 120.60 127.21 -6.61 1.60e+00 3.91e-01 1.71e+01 ... (remaining 12030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 4701 17.11 - 34.23: 435 34.23 - 51.34: 93 51.34 - 68.45: 8 68.45 - 85.57: 10 Dihedral angle restraints: 5247 sinusoidal: 1964 harmonic: 3283 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 170.63 -77.63 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CA LYS A 10 " pdb=" C LYS A 10 " pdb=" N ALA A 11 " pdb=" CA ALA A 11 " ideal model delta harmonic sigma weight residual 180.00 149.00 31.00 0 5.00e+00 4.00e-02 3.84e+01 dihedral pdb=" CA LYS A 349 " pdb=" C LYS A 349 " pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 5244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1214 0.084 - 0.169: 164 0.169 - 0.253: 16 0.253 - 0.338: 2 0.338 - 0.422: 2 Chirality restraints: 1398 Sorted by residual: chirality pdb=" CB VAL A 201 " pdb=" CA VAL A 201 " pdb=" CG1 VAL A 201 " pdb=" CG2 VAL A 201 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB ILE B 338 " pdb=" CA ILE B 338 " pdb=" CG1 ILE B 338 " pdb=" CG2 ILE B 338 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 1395 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.032 2.00e-02 2.50e+03 2.61e-02 1.70e+01 pdb=" CG TRP B 332 " 0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET R 214 " 0.066 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO R 215 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.021 2.00e-02 2.50e+03 1.90e-02 7.22e+00 pdb=" CG TYR B 105 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.001 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1297 2.75 - 3.29: 8569 3.29 - 3.83: 14672 3.83 - 4.36: 17392 4.36 - 4.90: 30149 Nonbonded interactions: 72079 Sorted by model distance: nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.215 2.440 nonbonded pdb=" O ILE E 100 " pdb=" OG SER E 105 " model vdw 2.234 2.440 nonbonded pdb=" O ALA R 419 " pdb=" OG1 THR R 423 " model vdw 2.241 2.440 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.242 2.440 nonbonded pdb=" O VAL R 386 " pdb=" OG1 THR R 390 " model vdw 2.250 2.440 ... (remaining 72074 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: 0.620 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: 3.200 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.630 Find NCS groups from input model: 0.250 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 0.099 8871 Z= 0.463 Angle : 1.118 16.879 12035 Z= 0.604 Chirality : 0.060 0.422 1398 Planarity : 0.007 0.098 1505 Dihedral : 13.790 85.567 3117 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.25 (0.23), residues: 1113 helix: -1.02 (0.24), residues: 357 sheet: -1.36 (0.33), residues: 251 loop : -1.81 (0.25), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.004 TRP B 332 HIS 0.013 0.003 HIS B 183 PHE 0.034 0.003 PHE A 323 TYR 0.047 0.003 TYR B 105 ARG 0.028 0.002 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 0.948 Fit side-chains REVERT: A 303 ILE cc_start: 0.7538 (mt) cc_final: 0.7302 (mm) REVERT: A 333 GLN cc_start: 0.7610 (mm-40) cc_final: 0.7379 (tp40) REVERT: A 337 ASP cc_start: 0.7943 (m-30) cc_final: 0.7657 (m-30) REVERT: R 214 MET cc_start: 0.6920 (ttm) cc_final: 0.6566 (ttp) REVERT: R 221 TYR cc_start: 0.7337 (t80) cc_final: 0.6873 (t80) REVERT: R 222 LEU cc_start: 0.6161 (mm) cc_final: 0.5681 (mm) REVERT: B 43 ILE cc_start: 0.8389 (mt) cc_final: 0.8066 (mt) REVERT: E 223 TYR cc_start: 0.7885 (m-80) cc_final: 0.7077 (m-80) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.2146 time to fit residues: 68.0606 Evaluate side-chains 197 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.0870 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 322 HIS ** R 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 220 GLN B 266 HIS ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8871 Z= 0.223 Angle : 0.667 10.091 12035 Z= 0.352 Chirality : 0.044 0.279 1398 Planarity : 0.005 0.065 1505 Dihedral : 5.757 25.837 1224 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 2.05 % Allowed : 9.08 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -1.25 (0.24), residues: 1113 helix: 0.56 (0.26), residues: 337 sheet: -1.12 (0.33), residues: 243 loop : -1.59 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 332 HIS 0.004 0.001 HIS B 183 PHE 0.030 0.002 PHE R 439 TYR 0.019 0.002 TYR B 105 ARG 0.007 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 303 ILE cc_start: 0.7589 (mt) cc_final: 0.7374 (mm) REVERT: A 337 ASP cc_start: 0.7944 (m-30) cc_final: 0.7663 (m-30) REVERT: R 187 ILE cc_start: 0.6995 (mm) cc_final: 0.6673 (mt) REVERT: R 214 MET cc_start: 0.6936 (ttm) cc_final: 0.6526 (ttm) REVERT: E 47 TRP cc_start: 0.6952 (t60) cc_final: 0.6535 (t60) REVERT: E 58 ILE cc_start: 0.7917 (mt) cc_final: 0.7688 (mt) REVERT: E 108 PHE cc_start: 0.7753 (m-80) cc_final: 0.7490 (m-80) outliers start: 19 outliers final: 16 residues processed: 215 average time/residue: 0.2228 time to fit residues: 64.8215 Evaluate side-chains 198 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 160 ILE Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 213 HIS A 333 GLN ** R 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8871 Z= 0.220 Angle : 0.635 8.133 12035 Z= 0.332 Chirality : 0.043 0.246 1398 Planarity : 0.004 0.054 1505 Dihedral : 5.372 24.968 1224 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.81 % Allowed : 12.76 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.24), residues: 1113 helix: 0.99 (0.26), residues: 345 sheet: -1.03 (0.32), residues: 257 loop : -1.38 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 332 HIS 0.008 0.001 HIS A 188 PHE 0.023 0.002 PHE A 334 TYR 0.016 0.001 TYR B 105 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 211 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7645 (mmp) cc_final: 0.6866 (mmp) REVERT: A 303 ILE cc_start: 0.7567 (mt) cc_final: 0.7356 (mm) REVERT: A 337 ASP cc_start: 0.7926 (m-30) cc_final: 0.7600 (m-30) REVERT: R 187 ILE cc_start: 0.6984 (mm) cc_final: 0.6638 (mt) REVERT: R 214 MET cc_start: 0.7174 (ttm) cc_final: 0.6760 (ttm) REVERT: E 47 TRP cc_start: 0.6759 (t60) cc_final: 0.6263 (t60) REVERT: E 58 ILE cc_start: 0.7918 (mt) cc_final: 0.7690 (mt) REVERT: E 108 PHE cc_start: 0.7768 (m-80) cc_final: 0.7482 (m-80) outliers start: 26 outliers final: 19 residues processed: 222 average time/residue: 0.2226 time to fit residues: 66.6377 Evaluate side-chains 207 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 0.0670 chunk 11 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8871 Z= 0.203 Angle : 0.623 7.996 12035 Z= 0.323 Chirality : 0.043 0.232 1398 Planarity : 0.004 0.049 1505 Dihedral : 5.230 24.135 1224 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.57 % Favored : 94.34 % Rotamer: Outliers : 2.70 % Allowed : 15.35 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.64 (0.24), residues: 1113 helix: 1.24 (0.26), residues: 342 sheet: -0.95 (0.32), residues: 261 loop : -1.26 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 332 HIS 0.003 0.001 HIS E 155 PHE 0.031 0.002 PHE R 439 TYR 0.016 0.001 TYR R 242 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 GLN cc_start: 0.8019 (tp-100) cc_final: 0.7723 (tp40) REVERT: A 337 ASP cc_start: 0.7898 (m-30) cc_final: 0.7326 (m-30) REVERT: R 187 ILE cc_start: 0.6839 (mm) cc_final: 0.6493 (mt) REVERT: R 214 MET cc_start: 0.7314 (ttm) cc_final: 0.6981 (ttm) REVERT: B 82 TRP cc_start: 0.6998 (m100) cc_final: 0.6362 (m100) REVERT: C 32 LYS cc_start: 0.8395 (ttmm) cc_final: 0.8175 (tppt) REVERT: E 47 TRP cc_start: 0.6689 (t60) cc_final: 0.6201 (t60) REVERT: E 58 ILE cc_start: 0.7843 (mt) cc_final: 0.7601 (mt) REVERT: E 108 PHE cc_start: 0.7743 (m-80) cc_final: 0.7486 (m-80) outliers start: 25 outliers final: 21 residues processed: 226 average time/residue: 0.2279 time to fit residues: 68.9430 Evaluate side-chains 225 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 355 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain R residue 435 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN E 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 8871 Z= 0.351 Angle : 0.711 8.608 12035 Z= 0.370 Chirality : 0.046 0.306 1398 Planarity : 0.004 0.045 1505 Dihedral : 5.636 29.153 1224 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.92 % Favored : 92.99 % Rotamer: Outliers : 4.00 % Allowed : 16.65 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.88 (0.24), residues: 1113 helix: 1.03 (0.26), residues: 350 sheet: -1.15 (0.32), residues: 261 loop : -1.39 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 258 HIS 0.006 0.002 HIS A 244 PHE 0.031 0.002 PHE R 439 TYR 0.020 0.002 TYR B 105 ARG 0.008 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 208 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7960 (mmm) cc_final: 0.7206 (mpp) REVERT: A 303 ILE cc_start: 0.7666 (mt) cc_final: 0.7460 (mm) REVERT: A 333 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7761 (tp40) REVERT: A 337 ASP cc_start: 0.7884 (m-30) cc_final: 0.7372 (m-30) REVERT: R 187 ILE cc_start: 0.6889 (mm) cc_final: 0.6546 (mt) REVERT: R 214 MET cc_start: 0.7440 (ttm) cc_final: 0.7107 (ttm) REVERT: R 253 MET cc_start: 0.7882 (tpp) cc_final: 0.7356 (tpp) REVERT: B 183 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.6598 (m170) REVERT: C 21 MET cc_start: 0.4435 (tmm) cc_final: 0.3793 (tmm) REVERT: E 47 TRP cc_start: 0.6752 (t60) cc_final: 0.6251 (t60) REVERT: E 108 PHE cc_start: 0.7849 (m-80) cc_final: 0.7496 (m-80) outliers start: 37 outliers final: 26 residues processed: 226 average time/residue: 0.2165 time to fit residues: 66.2701 Evaluate side-chains 226 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 220 VAL Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 62 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 102 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8871 Z= 0.203 Angle : 0.631 9.334 12035 Z= 0.327 Chirality : 0.043 0.246 1398 Planarity : 0.004 0.042 1505 Dihedral : 5.213 24.771 1224 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.39 % Favored : 94.52 % Rotamer: Outliers : 2.92 % Allowed : 17.84 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.55 (0.25), residues: 1113 helix: 1.35 (0.26), residues: 348 sheet: -1.00 (0.32), residues: 262 loop : -1.20 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.033 0.002 PHE A 323 TYR 0.016 0.001 TYR R 242 ARG 0.008 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 213 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.7923 (mmm) cc_final: 0.7193 (mpp) REVERT: A 247 MET cc_start: 0.7424 (mmp) cc_final: 0.6481 (mmp) REVERT: A 333 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7766 (tp40) REVERT: A 337 ASP cc_start: 0.7792 (m-30) cc_final: 0.7505 (m-30) REVERT: R 187 ILE cc_start: 0.6833 (mm) cc_final: 0.6514 (mp) REVERT: R 214 MET cc_start: 0.7363 (ttm) cc_final: 0.7054 (ttm) REVERT: B 183 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.7110 (m170) REVERT: B 254 ASP cc_start: 0.7899 (t0) cc_final: 0.7670 (t0) REVERT: E 58 ILE cc_start: 0.7849 (mt) cc_final: 0.7619 (mt) REVERT: E 108 PHE cc_start: 0.7703 (m-80) cc_final: 0.7413 (m-80) REVERT: E 205 SER cc_start: 0.8340 (m) cc_final: 0.8083 (p) outliers start: 27 outliers final: 22 residues processed: 224 average time/residue: 0.2247 time to fit residues: 67.7652 Evaluate side-chains 233 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8871 Z= 0.223 Angle : 0.642 8.830 12035 Z= 0.333 Chirality : 0.043 0.272 1398 Planarity : 0.004 0.053 1505 Dihedral : 5.202 25.695 1224 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 3.03 % Allowed : 19.14 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.25), residues: 1113 helix: 1.37 (0.26), residues: 350 sheet: -1.02 (0.32), residues: 266 loop : -1.14 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 47 HIS 0.003 0.001 HIS E 155 PHE 0.035 0.002 PHE A 323 TYR 0.016 0.001 TYR R 242 ARG 0.011 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 212 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7408 (mmp) cc_final: 0.6615 (mmp) REVERT: A 333 GLN cc_start: 0.8068 (tp-100) cc_final: 0.7746 (tp40) REVERT: A 337 ASP cc_start: 0.7779 (m-30) cc_final: 0.7471 (m-30) REVERT: R 187 ILE cc_start: 0.6818 (mm) cc_final: 0.6500 (mp) REVERT: R 214 MET cc_start: 0.7379 (ttm) cc_final: 0.7089 (ttm) REVERT: R 438 ASN cc_start: 0.5932 (m-40) cc_final: 0.5691 (t0) REVERT: B 183 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6969 (m170) REVERT: E 47 TRP cc_start: 0.6763 (t60) cc_final: 0.6274 (t60) REVERT: E 58 ILE cc_start: 0.7908 (mt) cc_final: 0.7659 (mt) REVERT: E 108 PHE cc_start: 0.7708 (m-80) cc_final: 0.7437 (m-80) REVERT: E 205 SER cc_start: 0.8346 (m) cc_final: 0.8101 (p) outliers start: 28 outliers final: 26 residues processed: 224 average time/residue: 0.2112 time to fit residues: 64.4721 Evaluate side-chains 229 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8871 Z= 0.272 Angle : 0.670 9.333 12035 Z= 0.346 Chirality : 0.045 0.329 1398 Planarity : 0.004 0.046 1505 Dihedral : 5.330 27.797 1224 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.29 % Favored : 93.62 % Rotamer: Outliers : 3.57 % Allowed : 19.46 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.59 (0.25), residues: 1113 helix: 1.31 (0.26), residues: 350 sheet: -0.99 (0.32), residues: 260 loop : -1.25 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 47 HIS 0.004 0.001 HIS A 188 PHE 0.035 0.002 PHE A 323 TYR 0.014 0.002 TYR R 242 ARG 0.009 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7529 (mmp) cc_final: 0.6827 (mmp) REVERT: A 337 ASP cc_start: 0.7808 (m-30) cc_final: 0.7497 (m-30) REVERT: R 214 MET cc_start: 0.7397 (ttm) cc_final: 0.7017 (ttm) REVERT: R 438 ASN cc_start: 0.5915 (m-40) cc_final: 0.5638 (t0) REVERT: B 142 HIS cc_start: 0.7804 (OUTLIER) cc_final: 0.7478 (m170) REVERT: B 183 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6920 (m170) REVERT: C 21 MET cc_start: 0.4359 (tmm) cc_final: 0.3793 (tmm) REVERT: E 47 TRP cc_start: 0.6732 (t60) cc_final: 0.6299 (t60) REVERT: E 108 PHE cc_start: 0.7804 (m-80) cc_final: 0.7455 (m-80) REVERT: E 205 SER cc_start: 0.8325 (m) cc_final: 0.8111 (p) outliers start: 33 outliers final: 26 residues processed: 216 average time/residue: 0.2167 time to fit residues: 63.8251 Evaluate side-chains 222 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain R residue 181 LEU Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.0980 chunk 30 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8871 Z= 0.197 Angle : 0.654 11.238 12035 Z= 0.332 Chirality : 0.043 0.262 1398 Planarity : 0.004 0.042 1505 Dihedral : 5.104 24.714 1224 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 3.14 % Allowed : 20.32 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.42 (0.25), residues: 1113 helix: 1.52 (0.26), residues: 344 sheet: -0.96 (0.32), residues: 264 loop : -1.13 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.002 0.001 HIS R 393 PHE 0.036 0.002 PHE A 323 TYR 0.017 0.001 TYR R 242 ARG 0.009 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 209 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7439 (mmp) cc_final: 0.6788 (mmp) REVERT: A 333 GLN cc_start: 0.8022 (tp-100) cc_final: 0.7683 (tp40) REVERT: A 337 ASP cc_start: 0.7768 (m-30) cc_final: 0.7468 (m-30) REVERT: R 214 MET cc_start: 0.7373 (ttm) cc_final: 0.7129 (ttm) REVERT: R 438 ASN cc_start: 0.5968 (m-40) cc_final: 0.5689 (t0) REVERT: B 183 HIS cc_start: 0.7446 (OUTLIER) cc_final: 0.6969 (m170) REVERT: C 21 MET cc_start: 0.4159 (tmm) cc_final: 0.3573 (tmm) REVERT: E 47 TRP cc_start: 0.6568 (t60) cc_final: 0.6183 (t60) REVERT: E 58 ILE cc_start: 0.7828 (mt) cc_final: 0.7573 (mt) REVERT: E 108 PHE cc_start: 0.7729 (m-80) cc_final: 0.7490 (m-80) outliers start: 29 outliers final: 25 residues processed: 222 average time/residue: 0.2062 time to fit residues: 62.5350 Evaluate side-chains 227 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 92 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8871 Z= 0.201 Angle : 0.663 11.319 12035 Z= 0.334 Chirality : 0.044 0.282 1398 Planarity : 0.004 0.061 1505 Dihedral : 5.012 24.866 1224 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 3.03 % Allowed : 20.54 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.37 (0.25), residues: 1113 helix: 1.60 (0.26), residues: 344 sheet: -0.98 (0.32), residues: 264 loop : -1.10 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.002 0.001 HIS R 393 PHE 0.035 0.002 PHE A 323 TYR 0.017 0.001 TYR R 242 ARG 0.014 0.001 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 MET cc_start: 0.7403 (mmp) cc_final: 0.6969 (mmp) REVERT: A 333 GLN cc_start: 0.8012 (tp-100) cc_final: 0.7683 (tp40) REVERT: A 337 ASP cc_start: 0.7744 (m-30) cc_final: 0.7463 (m-30) REVERT: R 214 MET cc_start: 0.7388 (ttm) cc_final: 0.7018 (ttm) REVERT: R 314 LEU cc_start: 0.6880 (tt) cc_final: 0.6472 (tp) REVERT: R 315 GLN cc_start: 0.6601 (mm110) cc_final: 0.5525 (mp10) REVERT: R 438 ASN cc_start: 0.5975 (m-40) cc_final: 0.5743 (t0) REVERT: B 183 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6920 (m170) REVERT: C 21 MET cc_start: 0.4262 (tmm) cc_final: 0.3708 (tmm) REVERT: E 47 TRP cc_start: 0.6611 (t60) cc_final: 0.6165 (t60) REVERT: E 58 ILE cc_start: 0.7823 (mt) cc_final: 0.7573 (mt) REVERT: E 108 PHE cc_start: 0.7785 (m-80) cc_final: 0.7506 (m-80) outliers start: 28 outliers final: 26 residues processed: 214 average time/residue: 0.2124 time to fit residues: 62.7681 Evaluate side-chains 224 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 197 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain R residue 296 ILE Chi-restraints excluded: chain R residue 341 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 397 LEU Chi-restraints excluded: chain R residue 425 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 268 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.201001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.157126 restraints weight = 10346.335| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.40 r_work: 0.3728 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8871 Z= 0.245 Angle : 0.684 10.973 12035 Z= 0.345 Chirality : 0.044 0.325 1398 Planarity : 0.004 0.062 1505 Dihedral : 5.134 26.561 1224 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.38 % Favored : 93.53 % Rotamer: Outliers : 3.03 % Allowed : 20.97 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1113 helix: 1.50 (0.26), residues: 350 sheet: -1.05 (0.32), residues: 266 loop : -1.16 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 47 HIS 0.003 0.001 HIS B 225 PHE 0.035 0.002 PHE A 323 TYR 0.015 0.001 TYR R 242 ARG 0.013 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.67 seconds wall clock time: 43 minutes 8.49 seconds (2588.49 seconds total)