Starting phenix.real_space_refine on Wed Mar 4 03:42:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kas_22782/03_2026/7kas_22782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kas_22782/03_2026/7kas_22782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kas_22782/03_2026/7kas_22782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kas_22782/03_2026/7kas_22782.map" model { file = "/net/cci-nas-00/data/ceres_data/7kas_22782/03_2026/7kas_22782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kas_22782/03_2026/7kas_22782.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.052 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 41 5.16 5 C 6915 2.51 5 N 1791 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10616 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3268 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 19, 'TRANS': 410} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 65 Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 435 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 229 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 30} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3804 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 27, 'TRANS': 456} Chain breaks: 3 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ASP:plan': 8, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "E" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1129 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 2, 'TRANS': 135} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1471 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 182} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 280 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'TRANS': 55} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 56 Planarities with less than four sites: {'UNK:plan-1': 56} Unresolved non-hydrogen planarities: 56 Time building chain proxies: 2.44, per 1000 atoms: 0.23 Number of scatterers: 10616 At special positions: 0 Unit cell: (110.67, 126.14, 135.66, 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 41 16.00 O 1869 8.00 N 1791 7.00 C 6915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.84 Conformation dependent library (CDL) restraints added in 513.0 milliseconds 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 70.8% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 28 through 47 removed outlier: 3.564A pdb=" N LYS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 47 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.577A pdb=" N ILE A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 174 removed outlier: 4.106A pdb=" N GLY A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 214 through 224 Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.130A pdb=" N VAL A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 260 removed outlier: 3.858A pdb=" N VAL A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 314 removed outlier: 3.563A pdb=" N MET A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 341 through 346 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.574A pdb=" N ASP A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 384 removed outlier: 3.604A pdb=" N THR A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 399 Processing helix chain 'A' and resid 409 through 415 Processing helix chain 'A' and resid 417 through 440 Processing helix chain 'A' and resid 444 through 466 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 43 through 80 removed outlier: 3.991A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N HIS C 72 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) Proline residue: C 74 - end of helix removed outlier: 3.548A pdb=" N VAL C 80 " --> pdb=" O ARG C 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 82 Processing helix chain 'D' and resid 13 through 36 removed outlier: 3.863A pdb=" N VAL D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) Proline residue: D 28 - end of helix Processing helix chain 'D' and resid 58 through 67 removed outlier: 4.484A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 65 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 94 through 112 Processing helix chain 'D' and resid 212 through 217 Processing helix chain 'D' and resid 219 through 233 removed outlier: 4.103A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.678A pdb=" N SER D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR D 249 " --> pdb=" O ARG D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.592A pdb=" N ALA D 259 " --> pdb=" O HIS D 255 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN D 268 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 removed outlier: 3.913A pdb=" N ILE D 280 " --> pdb=" O THR D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 removed outlier: 3.651A pdb=" N GLN D 292 " --> pdb=" O HIS D 288 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE D 293 " --> pdb=" O GLU D 289 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 288 through 294' Processing helix chain 'D' and resid 298 through 311 Processing helix chain 'D' and resid 318 through 343 removed outlier: 4.131A pdb=" N ARG D 324 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N HIS D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N SER D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU D 332 " --> pdb=" O LYS D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 362 Processing helix chain 'D' and resid 378 through 386 removed outlier: 4.571A pdb=" N THR D 384 " --> pdb=" O GLU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 397 Processing helix chain 'D' and resid 399 through 408 removed outlier: 3.988A pdb=" N GLY D 404 " --> pdb=" O ASP D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 423 removed outlier: 4.220A pdb=" N GLU D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 466 through 470 Processing helix chain 'D' and resid 480 through 486 removed outlier: 3.593A pdb=" N ASP D 486 " --> pdb=" O GLU D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 removed outlier: 4.311A pdb=" N MET D 491 " --> pdb=" O PRO D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 541 removed outlier: 4.493A pdb=" N ASN D 539 " --> pdb=" O SER D 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 86 removed outlier: 3.789A pdb=" N TYR E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE E 76 " --> pdb=" O HIS E 72 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 124 removed outlier: 4.155A pdb=" N LEU E 92 " --> pdb=" O HIS E 88 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) Proline residue: E 115 - end of helix Processing helix chain 'E' and resid 128 through 156 removed outlier: 3.642A pdb=" N LYS E 132 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 142 " --> pdb=" O VAL E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 182 removed outlier: 4.041A pdb=" N PHE E 172 " --> pdb=" O LYS E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.793A pdb=" N GLU E 188 " --> pdb=" O LEU E 184 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS E 190 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 203 removed outlier: 3.640A pdb=" N GLY E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 203 " --> pdb=" O ASN E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 199 through 203' Processing helix chain 'F' and resid 21 through 41 removed outlier: 3.564A pdb=" N GLU F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 71 removed outlier: 3.989A pdb=" N ASN F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU F 69 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLN F 70 " --> pdb=" O MET F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 91 removed outlier: 3.874A pdb=" N LYS F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 120 Proline residue: F 103 - end of helix Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 139 through 153 removed outlier: 4.008A pdb=" N VAL F 144 " --> pdb=" O PRO F 140 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ARG F 145 " --> pdb=" O ASP F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 168 Processing helix chain 'F' and resid 174 through 192 removed outlier: 3.923A pdb=" N ALA F 178 " --> pdb=" O MET F 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 170 Processing helix chain 'G' and resid 175 through 205 removed outlier: 3.573A pdb=" N UNK G 205 " --> pdb=" O UNK G 201 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 211 Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 284 Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AA4, first strand: chain 'D' and resid 450 through 453 removed outlier: 3.662A pdb=" N ILE D 571 " --> pdb=" O LEU D 453 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.522A pdb=" N ILE D 604 " --> pdb=" O VAL D 590 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 532 removed outlier: 3.804A pdb=" N GLY D 584 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 6 689 hydrogen bonds defined for protein. 2025 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: 1.52 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3355 1.34 - 1.46: 1582 1.46 - 1.57: 5818 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 10820 Sorted by residual: bond pdb=" C THR D 595 " pdb=" N ASP D 596 " ideal model delta sigma weight residual 1.333 1.317 0.016 1.41e-02 5.03e+03 1.36e+00 bond pdb=" CB TRP D 283 " pdb=" CG TRP D 283 " ideal model delta sigma weight residual 1.498 1.463 0.035 3.10e-02 1.04e+03 1.27e+00 bond pdb=" CB TRP D 513 " pdb=" CG TRP D 513 " ideal model delta sigma weight residual 1.498 1.467 0.031 3.10e-02 1.04e+03 1.01e+00 bond pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.62e-01 bond pdb=" N LEU F 102 " pdb=" CA LEU F 102 " ideal model delta sigma weight residual 1.463 1.457 0.007 6.90e-03 2.10e+04 8.92e-01 ... (remaining 10815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 14226 1.49 - 2.98: 375 2.98 - 4.47: 52 4.47 - 5.96: 19 5.96 - 7.45: 4 Bond angle restraints: 14676 Sorted by residual: angle pdb=" N VAL E 205 " pdb=" CA VAL E 205 " pdb=" C VAL E 205 " ideal model delta sigma weight residual 111.88 106.81 5.07 1.06e+00 8.90e-01 2.28e+01 angle pdb=" N VAL D 25 " pdb=" CA VAL D 25 " pdb=" C VAL D 25 " ideal model delta sigma weight residual 111.90 108.73 3.17 8.10e-01 1.52e+00 1.54e+01 angle pdb=" C GLU D 12 " pdb=" N THR D 13 " pdb=" CA THR D 13 " ideal model delta sigma weight residual 122.08 117.55 4.53 1.53e+00 4.27e-01 8.76e+00 angle pdb=" N PRO D 426 " pdb=" CA PRO D 426 " pdb=" C PRO D 426 " ideal model delta sigma weight residual 110.21 114.91 -4.70 1.64e+00 3.72e-01 8.21e+00 angle pdb=" C THR D 595 " pdb=" N ASP D 596 " pdb=" CA ASP D 596 " ideal model delta sigma weight residual 121.52 117.30 4.22 1.74e+00 3.30e-01 5.89e+00 ... (remaining 14671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5908 17.76 - 35.51: 506 35.51 - 53.27: 80 53.27 - 71.03: 14 71.03 - 88.78: 7 Dihedral angle restraints: 6515 sinusoidal: 2489 harmonic: 4026 Sorted by residual: dihedral pdb=" CA ARG F 154 " pdb=" C ARG F 154 " pdb=" N GLN F 155 " pdb=" CA GLN F 155 " ideal model delta harmonic sigma weight residual 180.00 162.70 17.30 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA LEU F 153 " pdb=" C LEU F 153 " pdb=" N ARG F 154 " pdb=" CA ARG F 154 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ARG D 509 " pdb=" C ARG D 509 " pdb=" N ARG D 510 " pdb=" CA ARG D 510 " ideal model delta harmonic sigma weight residual 180.00 163.19 16.81 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6512 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 986 0.028 - 0.056: 507 0.056 - 0.084: 160 0.084 - 0.112: 77 0.112 - 0.140: 21 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CB ILE E 170 " pdb=" CA ILE E 170 " pdb=" CG1 ILE E 170 " pdb=" CG2 ILE E 170 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.89e-01 chirality pdb=" CB VAL E 205 " pdb=" CA VAL E 205 " pdb=" CG1 VAL E 205 " pdb=" CG2 VAL E 205 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ILE D 470 " pdb=" N ILE D 470 " pdb=" C ILE D 470 " pdb=" CB ILE D 470 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1748 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 53 " 0.024 5.00e-02 4.00e+02 3.69e-02 2.18e+00 pdb=" N PRO B 54 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 366 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO D 367 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D 367 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 367 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 93 " -0.023 5.00e-02 4.00e+02 3.50e-02 1.96e+00 pdb=" N PRO F 94 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO F 94 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 94 " -0.020 5.00e-02 4.00e+02 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 299 2.71 - 3.26: 11030 3.26 - 3.80: 16319 3.80 - 4.35: 18560 4.35 - 4.90: 32083 Nonbonded interactions: 78291 Sorted by model distance: nonbonded pdb=" OE1 GLN D 370 " pdb=" OG1 THR D 391 " model vdw 2.162 3.040 nonbonded pdb=" ND2 ASN D 55 " pdb=" O LEU D 496 " model vdw 2.250 3.120 nonbonded pdb=" O TYR A 237 " pdb=" ND2 ASN A 243 " model vdw 2.269 3.120 nonbonded pdb=" O SER D 423 " pdb=" OG SER D 423 " model vdw 2.293 3.040 nonbonded pdb=" O PRO F 171 " pdb=" NH2 ARG F 177 " model vdw 2.293 3.120 ... (remaining 78286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.750 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 : 0.004 0.036 10820 Z= 0.178 Angle : 0.619 7.450 14676 Z= 0.349 Chirality : 0.040 0.140 1751 Planarity : 0.004 0.037 1831 Dihedral : 13.683 88.782 3899 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1305 helix: 0.09 (0.17), residues: 809 sheet: -2.52 (0.51), residues: 84 loop : -2.44 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.021 0.001 TYR F 190 PHE 0.010 0.001 PHE F 46 TRP 0.011 0.001 TRP D 14 HIS 0.006 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00390 (10820) covalent geometry : angle 0.61870 (14676) hydrogen bonds : bond 0.13342 ( 679) hydrogen bonds : angle 5.33566 ( 2025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 24 MET cc_start: 0.8717 (mmm) cc_final: 0.8412 (tpp) REVERT: E 73 ASP cc_start: 0.8497 (p0) cc_final: 0.8200 (p0) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1197 time to fit residues: 20.0956 Evaluate side-chains 64 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 427 ASN D 539 ASN D 558 HIS E 88 HIS F 68 ASN F 155 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.083505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.061442 restraints weight = 46052.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.063157 restraints weight = 24824.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.064244 restraints weight = 17231.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.064898 restraints weight = 13952.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.065135 restraints weight = 12389.666| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10820 Z= 0.147 Angle : 0.564 9.506 14676 Z= 0.286 Chirality : 0.039 0.158 1751 Planarity : 0.004 0.034 1831 Dihedral : 3.701 18.734 1463 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.36 % Allowed : 12.96 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1305 helix: 1.48 (0.18), residues: 817 sheet: -2.36 (0.48), residues: 94 loop : -1.98 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 154 TYR 0.015 0.001 TYR F 190 PHE 0.017 0.001 PHE A 256 TRP 0.013 0.001 TRP A 195 HIS 0.005 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00337 (10820) covalent geometry : angle 0.56424 (14676) hydrogen bonds : bond 0.04027 ( 679) hydrogen bonds : angle 3.92900 ( 2025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 373 CYS cc_start: 0.9343 (m) cc_final: 0.9110 (p) REVERT: B 64 PHE cc_start: 0.9177 (t80) cc_final: 0.8910 (t80) REVERT: D 24 MET cc_start: 0.8998 (mmm) cc_final: 0.8741 (tpp) REVERT: E 165 MET cc_start: 0.8135 (ttp) cc_final: 0.7402 (tmm) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.0890 time to fit residues: 12.2279 Evaluate side-chains 81 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 606 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 4 optimal weight: 0.0170 chunk 134 optimal weight: 50.0000 chunk 19 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 55 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.084630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.064735 restraints weight = 46296.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.064861 restraints weight = 29894.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.065974 restraints weight = 20655.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066152 restraints weight = 16435.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.066116 restraints weight = 15611.048| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10820 Z= 0.115 Angle : 0.525 9.692 14676 Z= 0.260 Chirality : 0.038 0.143 1751 Planarity : 0.004 0.040 1831 Dihedral : 3.513 17.759 1463 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.81 % Allowed : 15.05 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1305 helix: 1.97 (0.19), residues: 816 sheet: -1.99 (0.49), residues: 94 loop : -1.66 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 154 TYR 0.015 0.001 TYR E 121 PHE 0.014 0.001 PHE A 256 TRP 0.011 0.001 TRP F 95 HIS 0.006 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00260 (10820) covalent geometry : angle 0.52536 (14676) hydrogen bonds : bond 0.03542 ( 679) hydrogen bonds : angle 3.60335 ( 2025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8243 (tpt) cc_final: 0.7919 (tpt) REVERT: A 256 PHE cc_start: 0.8891 (t80) cc_final: 0.8535 (t80) REVERT: B 64 PHE cc_start: 0.8966 (t80) cc_final: 0.8542 (t80) REVERT: D 24 MET cc_start: 0.9013 (mmm) cc_final: 0.8597 (tpp) REVERT: E 165 MET cc_start: 0.8168 (ttp) cc_final: 0.7494 (tmm) outliers start: 20 outliers final: 16 residues processed: 95 average time/residue: 0.0858 time to fit residues: 12.5835 Evaluate side-chains 80 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 133 optimal weight: 40.0000 chunk 64 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 107 optimal weight: 8.9990 chunk 90 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 HIS E 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.078816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.058379 restraints weight = 45732.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.059160 restraints weight = 26899.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.059739 restraints weight = 19111.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.059887 restraints weight = 19161.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.059900 restraints weight = 16554.866| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 10820 Z= 0.342 Angle : 0.740 9.702 14676 Z= 0.377 Chirality : 0.045 0.219 1751 Planarity : 0.005 0.040 1831 Dihedral : 4.163 21.069 1463 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.26 % Allowed : 17.23 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.24), residues: 1305 helix: 1.60 (0.18), residues: 823 sheet: -1.98 (0.50), residues: 94 loop : -1.78 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 76 TYR 0.029 0.002 TYR F 190 PHE 0.029 0.002 PHE D 356 TRP 0.011 0.002 TRP A 326 HIS 0.005 0.001 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00784 (10820) covalent geometry : angle 0.74011 (14676) hydrogen bonds : bond 0.04796 ( 679) hydrogen bonds : angle 4.44454 ( 2025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 61 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7980 (tpt) cc_final: 0.7588 (tpt) REVERT: A 194 PHE cc_start: 0.9238 (OUTLIER) cc_final: 0.8913 (m-80) REVERT: D 24 MET cc_start: 0.9104 (mmm) cc_final: 0.8641 (tpp) REVERT: D 440 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7171 (mmm160) REVERT: D 526 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.7988 (pp) REVERT: E 98 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8741 (m110) REVERT: E 147 ASP cc_start: 0.8990 (m-30) cc_final: 0.8681 (p0) REVERT: E 165 MET cc_start: 0.8384 (ttp) cc_final: 0.8124 (tmm) REVERT: F 186 ASN cc_start: 0.9132 (OUTLIER) cc_final: 0.8494 (t0) outliers start: 47 outliers final: 31 residues processed: 101 average time/residue: 0.0804 time to fit residues: 12.6760 Evaluate side-chains 89 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 54 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 158 MET Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 26 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 93 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 132 optimal weight: 40.0000 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.083532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.061516 restraints weight = 46332.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.063073 restraints weight = 26356.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.064079 restraints weight = 18937.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.064572 restraints weight = 15517.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065042 restraints weight = 13983.992| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10820 Z= 0.127 Angle : 0.555 10.675 14676 Z= 0.276 Chirality : 0.039 0.190 1751 Planarity : 0.004 0.035 1831 Dihedral : 3.682 18.945 1463 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 2.90 % Allowed : 20.31 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1305 helix: 2.15 (0.18), residues: 819 sheet: -1.64 (0.52), residues: 94 loop : -1.56 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 30 TYR 0.015 0.001 TYR F 190 PHE 0.011 0.001 PHE A 256 TRP 0.012 0.001 TRP F 95 HIS 0.006 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00289 (10820) covalent geometry : angle 0.55451 (14676) hydrogen bonds : bond 0.03682 ( 679) hydrogen bonds : angle 3.68020 ( 2025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8109 (tpt) cc_final: 0.7730 (tpt) REVERT: A 256 PHE cc_start: 0.8930 (t80) cc_final: 0.8549 (t80) REVERT: A 373 CYS cc_start: 0.9205 (m) cc_final: 0.8974 (p) REVERT: A 400 MET cc_start: 0.9121 (mmm) cc_final: 0.8882 (mmm) REVERT: B 64 PHE cc_start: 0.9083 (t80) cc_final: 0.8689 (t80) REVERT: D 24 MET cc_start: 0.9116 (mmm) cc_final: 0.8654 (tpp) REVERT: D 440 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6846 (mmm160) REVERT: E 165 MET cc_start: 0.8107 (ttp) cc_final: 0.7739 (tmm) REVERT: F 186 ASN cc_start: 0.9124 (OUTLIER) cc_final: 0.8510 (t0) outliers start: 32 outliers final: 20 residues processed: 94 average time/residue: 0.0790 time to fit residues: 11.9141 Evaluate side-chains 84 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 63 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 334 HIS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 34 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.081857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.060261 restraints weight = 46545.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.061190 restraints weight = 29036.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062600 restraints weight = 18706.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.062449 restraints weight = 16510.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.062348 restraints weight = 15165.594| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10820 Z= 0.188 Angle : 0.591 10.303 14676 Z= 0.298 Chirality : 0.040 0.174 1751 Planarity : 0.004 0.035 1831 Dihedral : 3.749 18.112 1463 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.99 % Allowed : 21.49 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.24), residues: 1305 helix: 2.10 (0.18), residues: 812 sheet: -1.53 (0.54), residues: 94 loop : -1.40 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 76 TYR 0.021 0.001 TYR F 190 PHE 0.030 0.001 PHE A 395 TRP 0.008 0.001 TRP F 95 HIS 0.004 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00438 (10820) covalent geometry : angle 0.59116 (14676) hydrogen bonds : bond 0.03983 ( 679) hydrogen bonds : angle 3.82743 ( 2025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8097 (tpt) cc_final: 0.7700 (tpt) REVERT: A 256 PHE cc_start: 0.8979 (t80) cc_final: 0.8623 (t80) REVERT: B 64 PHE cc_start: 0.9153 (t80) cc_final: 0.8860 (t80) REVERT: D 24 MET cc_start: 0.9116 (mmm) cc_final: 0.8604 (tpp) REVERT: D 440 ARG cc_start: 0.7403 (mmm160) cc_final: 0.7124 (mmm160) REVERT: D 526 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.7936 (pp) REVERT: E 165 MET cc_start: 0.8230 (ttp) cc_final: 0.7925 (tmm) REVERT: F 186 ASN cc_start: 0.9126 (OUTLIER) cc_final: 0.8508 (t0) outliers start: 33 outliers final: 24 residues processed: 92 average time/residue: 0.0780 time to fit residues: 11.4345 Evaluate side-chains 85 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 0.0470 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 50.0000 chunk 40 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 311 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 = 0.3716 r_free = 0.3716 target = 0.080116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.059924 restraints weight = 45234.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.060815 restraints weight = 27092.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.061398 restraints weight = 18698.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.061535 restraints weight = 19057.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.061554 restraints weight = 16285.017| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10820 Z= 0.220 Angle : 0.637 10.822 14676 Z= 0.320 Chirality : 0.042 0.173 1751 Planarity : 0.004 0.037 1831 Dihedral : 3.906 19.156 1463 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.99 % Allowed : 22.21 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.24), residues: 1305 helix: 1.97 (0.18), residues: 816 sheet: -1.51 (0.55), residues: 94 loop : -1.41 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 76 TYR 0.023 0.002 TYR F 190 PHE 0.021 0.002 PHE A 395 TRP 0.008 0.001 TRP D 513 HIS 0.004 0.001 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00512 (10820) covalent geometry : angle 0.63728 (14676) hydrogen bonds : bond 0.04162 ( 679) hydrogen bonds : angle 3.95025 ( 2025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 62 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8199 (tpt) cc_final: 0.7850 (tpt) REVERT: A 256 PHE cc_start: 0.8957 (t80) cc_final: 0.8620 (t80) REVERT: A 373 CYS cc_start: 0.9210 (m) cc_final: 0.9005 (p) REVERT: B 64 PHE cc_start: 0.9107 (t80) cc_final: 0.8824 (t80) REVERT: D 24 MET cc_start: 0.9120 (mmm) cc_final: 0.8585 (tpp) REVERT: D 440 ARG cc_start: 0.7417 (mmm160) cc_final: 0.7140 (mmm160) REVERT: D 526 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.7987 (pp) REVERT: E 165 MET cc_start: 0.8267 (ttp) cc_final: 0.7983 (tmm) REVERT: F 128 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8371 (t0) REVERT: F 186 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8483 (t0) outliers start: 44 outliers final: 35 residues processed: 99 average time/residue: 0.0754 time to fit residues: 12.1077 Evaluate side-chains 99 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 61 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 329 CYS Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 359 ILE Chi-restraints excluded: chain D residue 360 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 514 CYS Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain D residue 526 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain F residue 186 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 19 optimal weight: 0.0870 chunk 74 optimal weight: 0.5980 chunk 4 optimal weight: 0.0980 chunk 36 optimal weight: 20.0000 chunk 84 optimal weight: 0.2980 chunk 77 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 124 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 0.3980 chunk 23 optimal weight: 4.9990 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.084327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.063060 restraints weight = 46493.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.064699 restraints weight = 25775.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.065743 restraints weight = 18120.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.066275 restraints weight = 14757.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.066753 restraints weight = 13222.346| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 10820 Z= 0.106 Angle : 0.548 11.450 14676 Z= 0.270 Chirality : 0.039 0.165 1751 Planarity : 0.004 0.036 1831 Dihedral : 3.439 16.599 1463 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.72 % Allowed : 24.12 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.25), residues: 1305 helix: 2.27 (0.18), residues: 825 sheet: -1.16 (0.56), residues: 94 loop : -1.10 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 90 TYR 0.013 0.001 TYR E 121 PHE 0.018 0.001 PHE A 395 TRP 0.013 0.001 TRP E 159 HIS 0.009 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00223 (10820) covalent geometry : angle 0.54805 (14676) hydrogen bonds : bond 0.03173 ( 679) hydrogen bonds : angle 3.36755 ( 2025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8180 (tpt) cc_final: 0.7830 (tpt) REVERT: A 256 PHE cc_start: 0.9001 (t80) cc_final: 0.8676 (t80) REVERT: B 64 PHE cc_start: 0.8983 (t80) cc_final: 0.8355 (t80) REVERT: D 24 MET cc_start: 0.9026 (mmm) cc_final: 0.8665 (tpp) REVERT: D 440 ARG cc_start: 0.7221 (mmm160) cc_final: 0.6976 (mmm160) REVERT: D 608 MET cc_start: 0.8282 (ptm) cc_final: 0.8044 (ptp) REVERT: E 147 ASP cc_start: 0.8968 (m-30) cc_final: 0.8714 (p0) REVERT: E 165 MET cc_start: 0.8206 (ttp) cc_final: 0.7701 (tmm) REVERT: F 128 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8210 (t0) outliers start: 19 outliers final: 13 residues processed: 85 average time/residue: 0.0774 time to fit residues: 10.4984 Evaluate side-chains 76 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 85 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 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 = 0.3678 r_free = 0.3678 target = 0.080938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.058888 restraints weight = 46770.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.060254 restraints weight = 28482.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.061543 restraints weight = 19051.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.061652 restraints weight = 16266.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.061454 restraints weight = 14587.862| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 10820 Z= 0.275 Angle : 0.687 11.277 14676 Z= 0.347 Chirality : 0.043 0.172 1751 Planarity : 0.004 0.035 1831 Dihedral : 3.885 18.518 1463 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.18 % Allowed : 24.03 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.24), residues: 1305 helix: 1.95 (0.18), residues: 817 sheet: -1.31 (0.56), residues: 94 loop : -1.31 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 76 TYR 0.025 0.002 TYR F 190 PHE 0.021 0.002 PHE D 356 TRP 0.009 0.002 TRP D 283 HIS 0.003 0.001 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00643 (10820) covalent geometry : angle 0.68698 (14676) hydrogen bonds : bond 0.04285 ( 679) hydrogen bonds : angle 4.01560 ( 2025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8439 (tpt) cc_final: 0.8096 (tpt) REVERT: A 194 PHE cc_start: 0.9158 (OUTLIER) cc_final: 0.8808 (m-80) REVERT: B 64 PHE cc_start: 0.9170 (t80) cc_final: 0.8875 (t80) REVERT: D 24 MET cc_start: 0.9126 (mmm) cc_final: 0.8655 (tpp) REVERT: D 440 ARG cc_start: 0.7307 (mmm160) cc_final: 0.7077 (mmm160) REVERT: E 147 ASP cc_start: 0.8931 (m-30) cc_final: 0.8687 (p0) REVERT: E 165 MET cc_start: 0.8316 (ttp) cc_final: 0.7985 (tmm) outliers start: 24 outliers final: 21 residues processed: 78 average time/residue: 0.0740 time to fit residues: 9.4758 Evaluate side-chains 81 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain E residue 87 ILE Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 179 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 120 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 0.0000 chunk 5 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.083860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.063160 restraints weight = 46636.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.064041 restraints weight = 27239.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.065021 restraints weight = 18451.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065131 restraints weight = 15380.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.065210 restraints weight = 14652.880| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10820 Z= 0.111 Angle : 0.563 11.694 14676 Z= 0.277 Chirality : 0.039 0.163 1751 Planarity : 0.004 0.037 1831 Dihedral : 3.498 16.841 1463 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.72 % Allowed : 24.39 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.25), residues: 1305 helix: 2.19 (0.18), residues: 826 sheet: -1.10 (0.56), residues: 94 loop : -0.98 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 589 TYR 0.014 0.001 TYR F 190 PHE 0.016 0.001 PHE A 395 TRP 0.014 0.001 TRP E 159 HIS 0.008 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00251 (10820) covalent geometry : angle 0.56330 (14676) hydrogen bonds : bond 0.03288 ( 679) hydrogen bonds : angle 3.39117 ( 2025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2610 Ramachandran restraints generated. 1305 Oldfield, 0 Emsley, 1305 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8246 (tpt) cc_final: 0.7908 (tpt) REVERT: A 256 PHE cc_start: 0.8925 (t80) cc_final: 0.8584 (t80) REVERT: A 260 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9203 (tp) REVERT: B 64 PHE cc_start: 0.8934 (t80) cc_final: 0.8322 (t80) REVERT: D 24 MET cc_start: 0.9051 (mmm) cc_final: 0.8636 (tpp) REVERT: D 440 ARG cc_start: 0.7360 (mmm160) cc_final: 0.7138 (mmm160) REVERT: E 147 ASP cc_start: 0.9001 (m-30) cc_final: 0.8738 (p0) REVERT: E 165 MET cc_start: 0.8248 (ttp) cc_final: 0.7796 (tmm) REVERT: F 128 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8112 (t0) outliers start: 19 outliers final: 14 residues processed: 85 average time/residue: 0.0780 time to fit residues: 10.8074 Evaluate side-chains 80 residues out of total 1163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 64 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 194 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain D residue 57 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 341 CYS Chi-restraints excluded: chain D residue 425 ILE Chi-restraints excluded: chain D residue 516 LEU Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 183 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 45 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 132 optimal weight: 50.0000 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.0870 chunk 89 optimal weight: 0.9980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 71 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.083878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.061976 restraints weight = 46789.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.063718 restraints weight = 25025.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.064846 restraints weight = 17245.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.065396 restraints weight = 13852.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.065897 restraints weight = 12367.199| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 10820 Z= 0.109 Angle : 0.560 11.420 14676 Z= 0.272 Chirality : 0.039 0.161 1751 Planarity : 0.004 0.035 1831 Dihedral : 3.350 16.329 1463 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.63 % Allowed : 24.75 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.25), residues: 1305 helix: 2.28 (0.18), residues: 823 sheet: -0.99 (0.56), residues: 94 loop : -0.89 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 76 TYR 0.017 0.001 TYR F 190 PHE 0.013 0.001 PHE A 395 TRP 0.010 0.001 TRP E 159 HIS 0.007 0.001 HIS D 309 Details of bonding type rmsd covalent geometry : bond 0.00249 (10820) covalent geometry : angle 0.56026 (14676) hydrogen bonds : bond 0.03195 ( 679) hydrogen bonds : angle 3.33991 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1677.35 seconds wall clock time: 29 minutes 42.24 seconds (1782.24 seconds total)