Starting phenix.real_space_refine on Mon Mar 11 12:31:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1r_31423/03_2024/7f1r_31423.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1r_31423/03_2024/7f1r_31423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1r_31423/03_2024/7f1r_31423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1r_31423/03_2024/7f1r_31423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1r_31423/03_2024/7f1r_31423.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f1r_31423/03_2024/7f1r_31423.pdb" } resolution = 3.0 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1639 atoms to isotropic. 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 52 5.16 5 C 4274 2.51 5 N 1110 2.21 5 O 1185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 155": "NH1" <-> "NH2" Residue "R ASP 171": "OD1" <-> "OD2" Residue "R ARG 235": "NH1" <-> "NH2" Residue "R TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 318": "NH1" <-> "NH2" Residue "R ARG 320": "NH1" <-> "NH2" Residue "R ARG 327": "NH1" <-> "NH2" Residue "R ARG 330": "NH1" <-> "NH2" Residue "R PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 357": "OE1" <-> "OE2" Residue "R ARG 369": "NH1" <-> "NH2" Residue "R GLU 378": "OE1" <-> "OE2" Residue "R PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 9": "OD1" <-> "OD2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 246": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6621 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2450 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 12, 'TRANS': 314} Chain breaks: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 138 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1627 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2305 Classifications: {'peptide': 316} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 109 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 78 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 239 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 4.13, per 1000 atoms: 0.62 Number of scatterers: 6621 At special positions: 0 Unit cell: (114.95, 121.22, 68.97, 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 52 16.00 O 1185 8.00 N 1110 7.00 C 4274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 10 " - pdb=" SG CYS R 34 " distance=2.03 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 267 " distance=2.03 Simple disulfide: pdb=" SG CYS R 196 " - pdb=" SG CYS R 273 " 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: 2.66 Conformation dependent library (CDL) restraints added in 1.4 seconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 9 sheets defined 43.2% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'R' and resid 3 through 7 Processing helix chain 'R' and resid 56 through 65 removed outlier: 4.064A pdb=" N LEU R 65 " --> pdb=" O TYR R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 153 removed outlier: 3.589A pdb=" N VAL R 146 " --> pdb=" O GLY R 142 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU R 150 " --> pdb=" O VAL R 146 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 176 removed outlier: 4.249A pdb=" N ILE R 162 " --> pdb=" O SER R 158 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR R 163 " --> pdb=" O MET R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 185 Processing helix chain 'R' and resid 193 through 226 Processing helix chain 'R' and resid 227 through 235 Processing helix chain 'R' and resid 236 through 261 Proline residue: R 257 - end of helix Processing helix chain 'R' and resid 281 through 317 removed outlier: 5.314A pdb=" N LEU R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 321 through 356 removed outlier: 3.606A pdb=" N ARG R 325 " --> pdb=" O ASN R 321 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS R 326 " --> pdb=" O GLU R 322 " (cutoff:3.500A) Proline residue: R 345 - end of helix removed outlier: 3.679A pdb=" N PHE R 355 " --> pdb=" O LEU R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 394 removed outlier: 4.074A pdb=" N ARG R 369 " --> pdb=" O SER R 365 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU R 370 " --> pdb=" O SER R 366 " (cutoff:3.500A) Proline residue: R 389 - end of helix Processing helix chain 'R' and resid 396 through 408 removed outlier: 3.727A pdb=" N TYR R 402 " --> pdb=" O LYS R 398 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 403 " --> pdb=" O PHE R 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 33 removed outlier: 3.660A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.626A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 272 through 281 removed outlier: 4.388A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.882A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.697A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.509A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.655A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.557A pdb=" N ALA C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 262 through 263 removed outlier: 3.911A pdb=" N ARG R 263 " --> pdb=" O SER R 274 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER R 274 " --> pdb=" O ARG R 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.507A pdb=" N MET A 198 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.984A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.524A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 5.910A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.433A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.349A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.629A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.860A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 975 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: 1.86 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2094 1.35 - 1.46: 1715 1.46 - 1.58: 2883 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 6762 Sorted by residual: bond pdb=" N ARG A 313 " pdb=" CA ARG A 313 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.27e-02 6.20e+03 5.48e+00 bond pdb=" N ARG B 304 " pdb=" CA ARG B 304 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.22e-02 6.72e+03 4.43e+00 bond pdb=" CA SER R 1 " pdb=" C SER R 1 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.10e-02 2.27e+03 7.37e-01 bond pdb=" CA LEU R 128 " pdb=" C LEU R 128 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.10e-02 2.27e+03 6.53e-01 bond pdb=" C PRO R 129 " pdb=" N PRO R 130 " ideal model delta sigma weight residual 1.336 1.345 -0.009 1.20e-02 6.94e+03 5.79e-01 ... (remaining 6757 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.19: 160 107.19 - 113.90: 3883 113.90 - 120.62: 2752 120.62 - 127.33: 2343 127.33 - 134.05: 68 Bond angle restraints: 9206 Sorted by residual: angle pdb=" N GLN R 281 " pdb=" CA GLN R 281 " pdb=" C GLN R 281 " ideal model delta sigma weight residual 110.44 107.09 3.35 1.20e+00 6.94e-01 7.80e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 121.54 126.67 -5.13 1.91e+00 2.74e-01 7.20e+00 angle pdb=" CA ARG A 313 " pdb=" C ARG A 313 " pdb=" O ARG A 313 " ideal model delta sigma weight residual 120.54 118.15 2.39 1.04e+00 9.25e-01 5.29e+00 angle pdb=" N VAL R 178 " pdb=" CA VAL R 178 " pdb=" C VAL R 178 " ideal model delta sigma weight residual 108.88 113.21 -4.33 2.16e+00 2.14e-01 4.01e+00 angle pdb=" CA VAL R 178 " pdb=" C VAL R 178 " pdb=" N PRO R 179 " ideal model delta sigma weight residual 118.88 121.94 -3.06 1.54e+00 4.22e-01 3.95e+00 ... (remaining 9201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.64: 3652 15.64 - 31.28: 236 31.28 - 46.92: 44 46.92 - 62.55: 10 62.55 - 78.19: 5 Dihedral angle restraints: 3947 sinusoidal: 1343 harmonic: 2604 Sorted by residual: dihedral pdb=" CB CYS R 196 " pdb=" SG CYS R 196 " pdb=" SG CYS R 273 " pdb=" CB CYS R 273 " ideal model delta sinusoidal sigma weight residual -86.00 -161.48 75.48 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 267 " pdb=" CB CYS R 267 " ideal model delta sinusoidal sigma weight residual -86.00 -35.92 -50.08 1 1.00e+01 1.00e-02 3.44e+01 dihedral pdb=" CB CYS R 11 " pdb=" SG CYS R 11 " pdb=" SG CYS R 50 " pdb=" CB CYS R 50 " ideal model delta sinusoidal sigma weight residual -86.00 -56.15 -29.85 1 1.00e+01 1.00e-02 1.27e+01 ... (remaining 3944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 643 0.025 - 0.050: 258 0.050 - 0.074: 119 0.074 - 0.099: 53 0.099 - 0.124: 25 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA LEU R 256 " pdb=" N LEU R 256 " pdb=" C LEU R 256 " pdb=" CB LEU R 256 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 chirality pdb=" CA ARG A 313 " pdb=" N ARG A 313 " pdb=" C ARG A 313 " pdb=" CB ARG A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.63 -0.12 2.00e-01 2.50e+01 3.55e-01 ... (remaining 1095 not shown) Planarity restraints: 1148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 256 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO R 257 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO R 257 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 257 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 128 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.29e+00 pdb=" N PRO R 129 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO R 129 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 129 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 303 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C ASP B 303 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP B 303 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG B 304 " 0.008 2.00e-02 2.50e+03 ... (remaining 1145 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1092 2.76 - 3.29: 6494 3.29 - 3.83: 11101 3.83 - 4.36: 12892 4.36 - 4.90: 22626 Nonbonded interactions: 54205 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.224 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.256 2.440 nonbonded pdb=" O LEU R 150 " pdb=" N ARG R 155 " model vdw 2.266 2.520 nonbonded pdb=" OE1 GLN B 176 " pdb=" OG1 THR B 179 " model vdw 2.279 2.440 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.321 2.520 ... (remaining 54200 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 3.970 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.410 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 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 : 0.002 0.030 6762 Z= 0.122 Angle : 0.484 6.596 9206 Z= 0.283 Chirality : 0.038 0.124 1098 Planarity : 0.003 0.039 1148 Dihedral : 11.209 78.194 2243 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.46 % Allowed : 1.83 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.24), residues: 872 helix: -1.30 (0.23), residues: 354 sheet: -0.71 (0.44), residues: 138 loop : -1.81 (0.26), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 339 HIS 0.002 0.000 HIS R 276 PHE 0.006 0.001 PHE B 234 TYR 0.005 0.001 TYR R 27 ARG 0.001 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 157 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 195 MET cc_start: 0.7308 (tmm) cc_final: 0.7011 (tmm) REVERT: R 369 ARG cc_start: 0.5788 (mmm-85) cc_final: 0.4496 (tpt170) REVERT: A 198 MET cc_start: 0.7252 (mpp) cc_final: 0.6982 (mpt) REVERT: A 267 PHE cc_start: 0.7686 (m-10) cc_final: 0.7310 (m-10) REVERT: A 296 TYR cc_start: 0.7637 (t80) cc_final: 0.7280 (t80) outliers start: 3 outliers final: 0 residues processed: 158 average time/residue: 0.9654 time to fit residues: 161.9515 Evaluate side-chains 111 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 41 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 265 GLN ** R 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 62 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6762 Z= 0.230 Angle : 0.595 8.529 9206 Z= 0.297 Chirality : 0.042 0.165 1098 Planarity : 0.004 0.036 1148 Dihedral : 3.404 13.919 941 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.83 % Allowed : 15.90 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.27), residues: 872 helix: 0.64 (0.27), residues: 354 sheet: -0.51 (0.40), residues: 169 loop : -1.18 (0.30), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 311 PHE 0.014 0.001 PHE A 196 TYR 0.016 0.002 TYR A 230 ARG 0.008 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 0.684 Fit side-chains REVERT: R 144 MET cc_start: 0.7118 (mmt) cc_final: 0.6667 (mmm) REVERT: R 195 MET cc_start: 0.7338 (tmm) cc_final: 0.7032 (tmm) REVERT: R 369 ARG cc_start: 0.5973 (mmm-85) cc_final: 0.4617 (tpt170) REVERT: A 24 ARG cc_start: 0.6997 (mtp-110) cc_final: 0.6492 (mtm-85) REVERT: A 296 TYR cc_start: 0.7933 (t80) cc_final: 0.7410 (t80) outliers start: 12 outliers final: 6 residues processed: 139 average time/residue: 0.9546 time to fit residues: 141.0655 Evaluate side-chains 122 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 116 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 145 LEU Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 276 HIS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain B residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 53 optimal weight: 0.0470 chunk 21 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 227 HIS R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 GLN B 230 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6762 Z= 0.313 Angle : 0.625 7.123 9206 Z= 0.321 Chirality : 0.043 0.157 1098 Planarity : 0.004 0.037 1148 Dihedral : 3.830 14.485 941 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.05 % Allowed : 18.65 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.28), residues: 872 helix: 1.38 (0.28), residues: 346 sheet: -0.12 (0.42), residues: 161 loop : -1.11 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 99 HIS 0.004 0.001 HIS A 188 PHE 0.015 0.002 PHE R 213 TYR 0.015 0.002 TYR B 59 ARG 0.006 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 0.739 Fit side-chains REVERT: R 129 PRO cc_start: 0.5918 (Cg_exo) cc_final: 0.5540 (Cg_endo) REVERT: R 144 MET cc_start: 0.7172 (mmt) cc_final: 0.6829 (mmm) REVERT: R 151 ILE cc_start: 0.5513 (OUTLIER) cc_final: 0.5287 (pp) REVERT: R 195 MET cc_start: 0.7357 (tmm) cc_final: 0.6975 (tmm) REVERT: R 261 PHE cc_start: 0.7452 (m-10) cc_final: 0.7177 (m-10) REVERT: R 336 MET cc_start: 0.7097 (mtp) cc_final: 0.6829 (mtp) REVERT: R 369 ARG cc_start: 0.6005 (mmm-85) cc_final: 0.4879 (tpt170) REVERT: R 384 HIS cc_start: 0.8447 (t-90) cc_final: 0.8172 (t-90) REVERT: A 46 LYS cc_start: 0.6780 (mptt) cc_final: 0.6431 (mptt) REVERT: A 186 GLU cc_start: 0.7013 (tt0) cc_final: 0.6692 (mt-10) REVERT: A 202 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8034 (p) outliers start: 33 outliers final: 10 residues processed: 139 average time/residue: 0.8640 time to fit residues: 128.6423 Evaluate side-chains 111 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 276 HIS Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 79 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6762 Z= 0.213 Angle : 0.566 8.317 9206 Z= 0.284 Chirality : 0.042 0.142 1098 Planarity : 0.003 0.038 1148 Dihedral : 3.689 15.077 941 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.50 % Allowed : 20.95 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.29), residues: 872 helix: 1.82 (0.28), residues: 345 sheet: -0.28 (0.41), residues: 174 loop : -0.97 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.004 0.001 HIS C 44 PHE 0.011 0.001 PHE R 213 TYR 0.011 0.001 TYR B 124 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 105 time to evaluate : 0.783 Fit side-chains revert: symmetry clash REVERT: R 129 PRO cc_start: 0.6086 (Cg_exo) cc_final: 0.5705 (Cg_endo) REVERT: R 144 MET cc_start: 0.7338 (mmt) cc_final: 0.7136 (mmm) REVERT: R 159 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7004 (tmt) REVERT: R 195 MET cc_start: 0.7392 (tmm) cc_final: 0.6842 (tmm) REVERT: R 261 PHE cc_start: 0.7601 (m-10) cc_final: 0.7263 (m-10) REVERT: R 314 LYS cc_start: 0.7723 (ttmm) cc_final: 0.7446 (ttmp) REVERT: R 336 MET cc_start: 0.6963 (mtp) cc_final: 0.6752 (mtp) REVERT: R 369 ARG cc_start: 0.6085 (mmm-85) cc_final: 0.4850 (tpt170) REVERT: A 46 LYS cc_start: 0.6619 (mptt) cc_final: 0.6257 (mptt) outliers start: 36 outliers final: 12 residues processed: 125 average time/residue: 0.9277 time to fit residues: 123.8853 Evaluate side-chains 107 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 47 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 258 ASN R 347 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6762 Z= 0.351 Angle : 0.630 7.299 9206 Z= 0.322 Chirality : 0.044 0.164 1098 Planarity : 0.004 0.038 1148 Dihedral : 4.038 16.285 941 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 5.20 % Allowed : 21.87 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.29), residues: 872 helix: 1.65 (0.28), residues: 348 sheet: -0.45 (0.39), residues: 176 loop : -0.93 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 99 HIS 0.004 0.001 HIS A 213 PHE 0.015 0.002 PHE R 213 TYR 0.011 0.002 TYR A 230 ARG 0.003 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 129 PRO cc_start: 0.5887 (Cg_exo) cc_final: 0.5459 (Cg_endo) REVERT: R 144 MET cc_start: 0.7439 (mmt) cc_final: 0.7235 (mmm) REVERT: R 159 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7089 (tmt) REVERT: R 195 MET cc_start: 0.7450 (tmm) cc_final: 0.6959 (tmm) REVERT: R 314 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7555 (ttmt) REVERT: R 369 ARG cc_start: 0.6222 (mmm-85) cc_final: 0.4942 (tpt170) outliers start: 34 outliers final: 18 residues processed: 129 average time/residue: 0.9693 time to fit residues: 133.1245 Evaluate side-chains 122 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 103 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6762 Z= 0.263 Angle : 0.603 9.383 9206 Z= 0.301 Chirality : 0.043 0.188 1098 Planarity : 0.004 0.038 1148 Dihedral : 3.971 19.714 941 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.96 % Allowed : 22.02 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.29), residues: 872 helix: 1.81 (0.28), residues: 344 sheet: -0.46 (0.40), residues: 174 loop : -0.97 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.019 0.001 PHE R 261 TYR 0.016 0.002 TYR B 264 ARG 0.003 0.000 ARG R 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 103 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 195 MET cc_start: 0.7539 (tmm) cc_final: 0.6992 (tmm) REVERT: R 369 ARG cc_start: 0.6272 (mmm-85) cc_final: 0.4989 (tpt170) REVERT: A 186 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7275 (tm-30) outliers start: 39 outliers final: 22 residues processed: 127 average time/residue: 1.0811 time to fit residues: 145.6287 Evaluate side-chains 119 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 391 ILE Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 52 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 347 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6762 Z= 0.251 Angle : 0.600 10.682 9206 Z= 0.299 Chirality : 0.042 0.138 1098 Planarity : 0.004 0.037 1148 Dihedral : 3.903 16.986 941 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 5.81 % Allowed : 23.39 % Favored : 70.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 872 helix: 1.86 (0.28), residues: 344 sheet: -0.54 (0.39), residues: 174 loop : -0.94 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 99 HIS 0.004 0.001 HIS B 183 PHE 0.023 0.001 PHE R 261 TYR 0.013 0.001 TYR B 264 ARG 0.003 0.000 ARG R 327 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 98 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 143 ASN cc_start: 0.7576 (m-40) cc_final: 0.7357 (m110) REVERT: R 144 MET cc_start: 0.7261 (tpt) cc_final: 0.6811 (mmm) REVERT: R 159 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.6894 (tmt) REVERT: R 195 MET cc_start: 0.7533 (tmm) cc_final: 0.7004 (tmm) REVERT: R 369 ARG cc_start: 0.6342 (mmm-85) cc_final: 0.5085 (tpt170) REVERT: A 186 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7269 (tm-30) outliers start: 38 outliers final: 21 residues processed: 125 average time/residue: 0.9803 time to fit residues: 130.3420 Evaluate side-chains 119 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 315 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 47 optimal weight: 0.1980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6762 Z= 0.196 Angle : 0.590 11.156 9206 Z= 0.291 Chirality : 0.042 0.237 1098 Planarity : 0.004 0.037 1148 Dihedral : 3.775 16.812 941 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.74 % Allowed : 24.31 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 872 helix: 2.07 (0.28), residues: 344 sheet: -0.50 (0.40), residues: 174 loop : -0.93 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 99 HIS 0.003 0.001 HIS B 183 PHE 0.030 0.001 PHE R 261 TYR 0.024 0.001 TYR R 346 ARG 0.003 0.000 ARG R 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 144 MET cc_start: 0.7297 (tpt) cc_final: 0.7069 (mmm) REVERT: R 195 MET cc_start: 0.7511 (tmm) cc_final: 0.6988 (tmm) REVERT: R 261 PHE cc_start: 0.8095 (m-10) cc_final: 0.7878 (m-10) REVERT: R 369 ARG cc_start: 0.6337 (mmm-85) cc_final: 0.5015 (tpt170) REVERT: A 14 GLU cc_start: 0.7158 (tm-30) cc_final: 0.6892 (tm-30) REVERT: B 59 TYR cc_start: 0.8325 (m-80) cc_final: 0.7842 (m-80) outliers start: 31 outliers final: 20 residues processed: 125 average time/residue: 0.9825 time to fit residues: 130.5825 Evaluate side-chains 119 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain R residue 402 TYR Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 34 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6762 Z= 0.356 Angle : 0.675 11.399 9206 Z= 0.336 Chirality : 0.045 0.225 1098 Planarity : 0.004 0.037 1148 Dihedral : 4.068 17.278 941 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.82 % Allowed : 25.69 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 872 helix: 1.79 (0.28), residues: 346 sheet: -0.60 (0.39), residues: 183 loop : -0.87 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 99 HIS 0.005 0.001 HIS B 183 PHE 0.022 0.002 PHE R 261 TYR 0.021 0.002 TYR B 264 ARG 0.004 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 144 MET cc_start: 0.7231 (tpt) cc_final: 0.6998 (mmm) REVERT: R 159 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7282 (tmt) REVERT: R 195 MET cc_start: 0.7537 (tmm) cc_final: 0.7034 (tmm) REVERT: R 369 ARG cc_start: 0.6377 (mmm-85) cc_final: 0.5093 (tpt170) REVERT: A 14 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6940 (tm-30) REVERT: B 59 TYR cc_start: 0.8670 (m-80) cc_final: 0.8344 (m-80) outliers start: 25 outliers final: 20 residues processed: 121 average time/residue: 0.9168 time to fit residues: 118.5282 Evaluate side-chains 116 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 319 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 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 86 optimal weight: 0.6980 chunk 79 optimal weight: 0.2980 chunk 69 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 0.0030 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 63 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 overall best weight: 0.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 347 ASN ** R 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6762 Z= 0.183 Angle : 0.609 12.165 9206 Z= 0.298 Chirality : 0.042 0.193 1098 Planarity : 0.004 0.037 1148 Dihedral : 3.854 18.974 941 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.14 % Allowed : 27.37 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.29), residues: 872 helix: 2.08 (0.28), residues: 345 sheet: -0.45 (0.41), residues: 172 loop : -0.95 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS R 384 PHE 0.010 0.001 PHE A 189 TYR 0.026 0.001 TYR R 346 ARG 0.004 0.000 ARG R 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 107 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 144 MET cc_start: 0.7238 (tpt) cc_final: 0.7033 (mmm) REVERT: R 195 MET cc_start: 0.7522 (tmm) cc_final: 0.7008 (tmm) REVERT: R 369 ARG cc_start: 0.6374 (mmm-85) cc_final: 0.5043 (tpt170) REVERT: A 14 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6957 (tm-30) REVERT: B 59 TYR cc_start: 0.8181 (m-80) cc_final: 0.7695 (m-80) outliers start: 14 outliers final: 12 residues processed: 118 average time/residue: 1.0435 time to fit residues: 130.6520 Evaluate side-chains 115 residues out of total 777 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 196 CYS Chi-restraints excluded: chain R residue 204 PHE Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 317 LEU Chi-restraints excluded: chain R residue 338 VAL Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 321 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 49 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 46 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 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.170963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131708 restraints weight = 7237.660| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.07 r_work: 0.3491 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6762 Z= 0.245 Angle : 0.619 11.196 9206 Z= 0.308 Chirality : 0.043 0.195 1098 Planarity : 0.004 0.037 1148 Dihedral : 3.894 20.973 941 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.75 % Allowed : 27.37 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.29), residues: 872 helix: 2.10 (0.28), residues: 344 sheet: -0.49 (0.41), residues: 178 loop : -0.91 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 99 HIS 0.005 0.001 HIS R 384 PHE 0.018 0.001 PHE R 136 TYR 0.017 0.001 TYR B 124 ARG 0.004 0.000 ARG R 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2848.73 seconds wall clock time: 51 minutes 21.64 seconds (3081.64 seconds total)