Starting phenix.real_space_refine on Sat Aug 23 10:18:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi3_33850/08_2025/7yi3_33850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi3_33850/08_2025/7yi3_33850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yi3_33850/08_2025/7yi3_33850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi3_33850/08_2025/7yi3_33850.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi3_33850/08_2025/7yi3_33850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi3_33850/08_2025/7yi3_33850.cif" } resolution = 3.3 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Zn 5 6.06 5 S 66 5.16 5 C 7300 2.51 5 N 1919 2.21 5 O 2135 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11425 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4258 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 7, 'TRANS': 498} Chain breaks: 5 Chain: "B" Number of atoms: 2923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2923 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 15, 'TRANS': 352} Chain: "C" Number of atoms: 1473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1473 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 174} Chain: "D" Number of atoms: 2588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2588 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 298} Chain breaks: 5 Chain: "E" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 178 Classifications: {'peptide': 20} Link IDs: {'TRANS': 19} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10169 SG CYS D 417 69.984 60.745 32.968 1.00 40.15 S ATOM 10196 SG CYS D 420 71.715 57.465 33.828 1.00 55.87 S ATOM 10452 SG CYS D 451 71.468 60.228 36.443 1.00 62.19 S ATOM 9108 SG CYS D 263 35.162 94.931 38.011 1.00 93.60 S ATOM 9125 SG CYS D 266 38.264 92.690 37.687 1.00 76.39 S ATOM 9278 SG CYS D 286 38.493 95.811 39.869 1.00 74.17 S ATOM 9413 SG CYS D 303 27.320 102.172 35.913 1.00108.66 S ATOM 9436 SG CYS D 306 23.561 104.664 35.015 1.00110.05 S ATOM 10357 SG CYS D 440 64.800 70.261 28.800 1.00 45.36 S ATOM 10383 SG CYS D 443 67.690 69.873 26.226 1.00 52.08 S ATOM 10572 SG CYS D 466 68.566 70.907 29.657 1.00 62.77 S Time building chain proxies: 3.11, per 1000 atoms: 0.27 Number of scatterers: 11425 At special positions: 0 Unit cell: (120.157, 139.643, 107.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 5 29.99 S 66 16.00 O 2135 8.00 N 1919 7.00 C 7300 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: 1.06 Conformation dependent library (CDL) restraints added in 696.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 188 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 420 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 417 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 451 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" ND1 HIS D 283 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 286 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 263 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 303 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 306 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 440 " Number of angles added : 9 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2652 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 7 sheets defined 54.5% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 678 through 694 removed outlier: 3.724A pdb=" N GLU A 684 " --> pdb=" O HIS A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.506A pdb=" N LEU A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 722 Processing helix chain 'A' and resid 759 through 763 Processing helix chain 'A' and resid 771 through 777 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.866A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 838 Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 891 through 922 removed outlier: 4.094A pdb=" N LYS A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 removed outlier: 3.884A pdb=" N LEU A 928 " --> pdb=" O PHE A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 934 removed outlier: 4.142A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 943 Processing helix chain 'A' and resid 944 through 961 Processing helix chain 'A' and resid 983 through 999 Processing helix chain 'A' and resid 1003 through 1023 Processing helix chain 'A' and resid 1141 through 1164 removed outlier: 4.157A pdb=" N MET A1164 " --> pdb=" O GLU A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1174 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 4.162A pdb=" N MET A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.682A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1259 Processing helix chain 'A' and resid 1259 through 1276 Processing helix chain 'A' and resid 1280 through 1294 removed outlier: 4.373A pdb=" N ILE A1284 " --> pdb=" O ALA A1280 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS A1293 " --> pdb=" O GLN A1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.794A pdb=" N TYR B 32 " --> pdb=" O VAL B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.858A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 79 through 87 Processing helix chain 'B' and resid 93 through 97 Processing helix chain 'B' and resid 98 through 105 Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.594A pdb=" N ARG B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.592A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 Processing helix chain 'B' and resid 343 through 348 removed outlier: 3.520A pdb=" N TYR B 346 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 381 Processing helix chain 'C' and resid 225 through 241 Processing helix chain 'C' and resid 253 through 267 removed outlier: 3.936A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 297 removed outlier: 3.798A pdb=" N LEU C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 279 " --> pdb=" O GLN C 275 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 316 removed outlier: 3.607A pdb=" N ASP C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.501A pdb=" N SER C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 369 removed outlier: 3.522A pdb=" N GLN C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.599A pdb=" N MET C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 171 through 175 Processing helix chain 'D' and resid 182 through 187 removed outlier: 4.419A pdb=" N GLY D 186 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 331 removed outlier: 3.758A pdb=" N LYS D 321 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN D 331 " --> pdb=" O ILE D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 344 removed outlier: 4.374A pdb=" N ASP D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 544 through 562 removed outlier: 3.668A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR D 549 " --> pdb=" O ASN D 545 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE D 552 " --> pdb=" O LYS D 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 563 Processing sheet with id=AA1, first strand: chain 'A' and resid 756 through 757 removed outlier: 3.566A pdb=" N VAL A 783 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 Processing sheet with id=AA3, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.866A pdb=" N VAL B 21 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N TYR B 64 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N TYR B 23 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 142 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 181 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLN B 270 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE B 183 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AA6, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA7, first strand: chain 'D' and resid 505 through 506 removed outlier: 3.778A pdb=" N TYR D 506 " --> pdb=" O ILE D 539 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1521 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: 1.92 Time building geometry restraints manager: 1.39 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: 3658 1.34 - 1.46: 2696 1.46 - 1.58: 5218 1.58 - 1.70: 0 1.70 - 1.81: 100 Bond restraints: 11672 Sorted by residual: bond pdb=" CG PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 1.503 1.380 0.123 3.40e-02 8.65e+02 1.31e+01 bond pdb=" CA GLU D 104 " pdb=" C GLU D 104 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.41e-02 5.03e+03 1.17e+00 bond pdb=" CG PRO D 119 " pdb=" CD PRO D 119 " ideal model delta sigma weight residual 1.503 1.538 -0.035 3.40e-02 8.65e+02 1.05e+00 bond pdb=" CG1 ILE A1018 " pdb=" CD1 ILE A1018 " ideal model delta sigma weight residual 1.513 1.477 0.036 3.90e-02 6.57e+02 8.75e-01 bond pdb=" C ARG A 907 " pdb=" O ARG A 907 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.49e-01 ... (remaining 11667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 15593 2.19 - 4.38: 111 4.38 - 6.57: 21 6.57 - 8.77: 3 8.77 - 10.96: 2 Bond angle restraints: 15730 Sorted by residual: angle pdb=" N PRO A 786 " pdb=" CD PRO A 786 " pdb=" CG PRO A 786 " ideal model delta sigma weight residual 103.20 92.52 10.68 1.50e+00 4.44e-01 5.07e+01 angle pdb=" CA PRO A 786 " pdb=" N PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 112.00 103.45 8.55 1.40e+00 5.10e-01 3.73e+01 angle pdb=" CA PRO A 786 " pdb=" CB PRO A 786 " pdb=" CG PRO A 786 " ideal model delta sigma weight residual 104.50 96.77 7.73 1.90e+00 2.77e-01 1.65e+01 angle pdb=" CB PRO A 786 " pdb=" CG PRO A 786 " pdb=" CD PRO A 786 " ideal model delta sigma weight residual 106.10 95.14 10.96 3.20e+00 9.77e-02 1.17e+01 angle pdb=" C VAL B 106 " pdb=" CA VAL B 106 " pdb=" CB VAL B 106 " ideal model delta sigma weight residual 111.29 116.84 -5.55 1.64e+00 3.72e-01 1.15e+01 ... (remaining 15725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 6009 17.16 - 34.31: 779 34.31 - 51.47: 190 51.47 - 68.63: 36 68.63 - 85.78: 14 Dihedral angle restraints: 7028 sinusoidal: 2926 harmonic: 4102 Sorted by residual: dihedral pdb=" CA TYR B 347 " pdb=" C TYR B 347 " pdb=" N GLY B 348 " pdb=" CA GLY B 348 " ideal model delta harmonic sigma weight residual 180.00 157.43 22.57 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA ILE C 335 " pdb=" C ILE C 335 " pdb=" N SER C 336 " pdb=" CA SER C 336 " ideal model delta harmonic sigma weight residual 180.00 158.82 21.18 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LYS B 153 " pdb=" C LYS B 153 " pdb=" N LYS B 154 " pdb=" CA LYS B 154 " ideal model delta harmonic sigma weight residual 180.00 159.43 20.57 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 7025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1127 0.035 - 0.069: 417 0.069 - 0.104: 108 0.104 - 0.139: 35 0.139 - 0.173: 1 Chirality restraints: 1688 Sorted by residual: chirality pdb=" CB ILE D 312 " pdb=" CA ILE D 312 " pdb=" CG1 ILE D 312 " pdb=" CG2 ILE D 312 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.50e-01 chirality pdb=" CG LEU A 689 " pdb=" CB LEU A 689 " pdb=" CD1 LEU A 689 " pdb=" CD2 LEU A 689 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CB VAL B 106 " pdb=" CA VAL B 106 " pdb=" CG1 VAL B 106 " pdb=" CG2 VAL B 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1685 not shown) Planarity restraints: 2005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.079 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO D 119 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO D 119 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 119 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 785 " -0.073 5.00e-02 4.00e+02 1.06e-01 1.78e+01 pdb=" N PRO A 786 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 786 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 786 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR D 439 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C THR D 439 " -0.038 2.00e-02 2.50e+03 pdb=" O THR D 439 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS D 440 " 0.013 2.00e-02 2.50e+03 ... (remaining 2002 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 99 2.59 - 3.17: 9437 3.17 - 3.75: 17650 3.75 - 4.32: 24863 4.32 - 4.90: 40761 Nonbonded interactions: 92810 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.014 2.230 nonbonded pdb=" OG SER C 313 " pdb=" O LYS C 318 " model vdw 2.090 3.040 nonbonded pdb=" OG SER B 123 " pdb=" OD2 ASP B 165 " model vdw 2.106 3.040 nonbonded pdb=" OD2 ASP B 244 " pdb=" OG SER B 287 " model vdw 2.167 3.040 nonbonded pdb=" O ILE C 342 " pdb=" OG1 THR C 345 " model vdw 2.184 3.040 ... (remaining 92805 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 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 : 0.003 0.123 11687 Z= 0.124 Angle : 0.527 10.958 15739 Z= 0.286 Chirality : 0.040 0.173 1688 Planarity : 0.005 0.120 2005 Dihedral : 16.299 85.785 4376 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.16 % Allowed : 21.13 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.30 (0.23), residues: 1362 helix: 0.85 (0.20), residues: 712 sheet: -0.58 (0.60), residues: 85 loop : -1.50 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 369 TYR 0.015 0.001 TYR B 347 PHE 0.018 0.001 PHE A1305 TRP 0.009 0.001 TRP B 261 HIS 0.003 0.001 HIS A1252 Details of bonding type rmsd covalent geometry : bond 0.00278 (11672) covalent geometry : angle 0.52315 (15730) hydrogen bonds : bond 0.14657 ( 531) hydrogen bonds : angle 6.03494 ( 1521) metal coordination : bond 0.00570 ( 15) metal coordination : angle 2.76105 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 1164 MET cc_start: 0.8311 (ptt) cc_final: 0.8083 (ptt) REVERT: D 548 LYS cc_start: 0.7389 (mtmt) cc_final: 0.6844 (mtmt) outliers start: 2 outliers final: 0 residues processed: 111 average time/residue: 0.1301 time to fit residues: 20.4187 Evaluate side-chains 105 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.0040 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN C 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.130922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.108069 restraints weight = 19060.869| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.93 r_work: 0.3352 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11687 Z= 0.121 Angle : 0.503 6.115 15739 Z= 0.269 Chirality : 0.040 0.147 1688 Planarity : 0.004 0.073 2005 Dihedral : 4.460 22.844 1511 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.04 % Allowed : 19.32 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.05 (0.23), residues: 1362 helix: 1.16 (0.19), residues: 704 sheet: -0.34 (0.62), residues: 84 loop : -1.35 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 369 TYR 0.016 0.001 TYR B 347 PHE 0.012 0.001 PHE A 995 TRP 0.006 0.001 TRP A1223 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00257 (11672) covalent geometry : angle 0.49930 (15730) hydrogen bonds : bond 0.04670 ( 531) hydrogen bonds : angle 4.56857 ( 1521) metal coordination : bond 0.00521 ( 15) metal coordination : angle 2.60228 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.458 Fit side-chains REVERT: A 1164 MET cc_start: 0.8383 (ptt) cc_final: 0.8169 (ptt) REVERT: A 1288 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6104 (mm) REVERT: D 116 ASN cc_start: 0.6775 (OUTLIER) cc_final: 0.6233 (t0) REVERT: D 310 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5484 (mm) REVERT: D 312 ILE cc_start: 0.5957 (OUTLIER) cc_final: 0.5609 (mt) REVERT: D 552 PHE cc_start: 0.7408 (m-80) cc_final: 0.7045 (m-10) outliers start: 26 outliers final: 12 residues processed: 138 average time/residue: 0.1139 time to fit residues: 22.7535 Evaluate side-chains 117 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 452 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 128 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.127939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.104918 restraints weight = 19567.716| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.95 r_work: 0.3298 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11687 Z= 0.194 Angle : 0.579 7.568 15739 Z= 0.307 Chirality : 0.042 0.156 1688 Planarity : 0.005 0.063 2005 Dihedral : 4.839 24.537 1511 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.14 % Allowed : 20.42 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.18 (0.23), residues: 1362 helix: 0.96 (0.19), residues: 706 sheet: -0.47 (0.62), residues: 84 loop : -1.44 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 369 TYR 0.022 0.002 TYR B 347 PHE 0.014 0.002 PHE D 308 TRP 0.008 0.001 TRP D 447 HIS 0.004 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00444 (11672) covalent geometry : angle 0.57386 (15730) hydrogen bonds : bond 0.05376 ( 531) hydrogen bonds : angle 4.64918 ( 1521) metal coordination : bond 0.00668 ( 15) metal coordination : angle 3.35331 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.486 Fit side-chains revert: symmetry clash REVERT: A 1164 MET cc_start: 0.8463 (ptt) cc_final: 0.8254 (ptt) REVERT: A 1288 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6055 (mm) REVERT: B 238 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7963 (mt) REVERT: D 116 ASN cc_start: 0.6952 (OUTLIER) cc_final: 0.6437 (t0) REVERT: D 312 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5667 (mt) REVERT: D 552 PHE cc_start: 0.7439 (m-10) cc_final: 0.7147 (m-10) outliers start: 40 outliers final: 21 residues processed: 142 average time/residue: 0.1072 time to fit residues: 22.5911 Evaluate side-chains 126 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 983 ASN Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 296 MET Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 470 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 129 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 82 optimal weight: 0.2980 chunk 32 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 0.0070 chunk 3 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 921 GLN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.130866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108046 restraints weight = 19380.947| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.97 r_work: 0.3349 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11687 Z= 0.106 Angle : 0.489 5.796 15739 Z= 0.260 Chirality : 0.039 0.153 1688 Planarity : 0.004 0.061 2005 Dihedral : 4.474 23.638 1511 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.51 % Allowed : 21.76 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.09 (0.23), residues: 1362 helix: 1.17 (0.19), residues: 711 sheet: -0.30 (0.63), residues: 84 loop : -1.33 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 369 TYR 0.014 0.001 TYR B 347 PHE 0.011 0.001 PHE A 995 TRP 0.006 0.001 TRP A1223 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00217 (11672) covalent geometry : angle 0.48558 (15730) hydrogen bonds : bond 0.04388 ( 531) hydrogen bonds : angle 4.37353 ( 1521) metal coordination : bond 0.00549 ( 15) metal coordination : angle 2.43075 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 818 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: A 1164 MET cc_start: 0.8386 (ptt) cc_final: 0.8166 (ptt) REVERT: D 312 ILE cc_start: 0.6119 (OUTLIER) cc_final: 0.5682 (mt) REVERT: D 552 PHE cc_start: 0.7427 (m-10) cc_final: 0.6960 (m-10) outliers start: 32 outliers final: 18 residues processed: 139 average time/residue: 0.1058 time to fit residues: 21.9871 Evaluate side-chains 122 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 102 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 516 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 116 ASN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.129961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.107123 restraints weight = 19290.051| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.95 r_work: 0.3334 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11687 Z= 0.131 Angle : 0.507 6.506 15739 Z= 0.269 Chirality : 0.040 0.162 1688 Planarity : 0.004 0.066 2005 Dihedral : 4.500 23.461 1511 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.67 % Allowed : 21.92 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.09 (0.23), residues: 1362 helix: 1.16 (0.19), residues: 712 sheet: -0.38 (0.58), residues: 94 loop : -1.32 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 369 TYR 0.018 0.001 TYR B 347 PHE 0.012 0.001 PHE D 308 TRP 0.006 0.001 TRP A1223 HIS 0.003 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00288 (11672) covalent geometry : angle 0.50272 (15730) hydrogen bonds : bond 0.04570 ( 531) hydrogen bonds : angle 4.36283 ( 1521) metal coordination : bond 0.00524 ( 15) metal coordination : angle 2.75698 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 1288 LEU cc_start: 0.6238 (OUTLIER) cc_final: 0.5936 (mm) REVERT: B 213 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: D 312 ILE cc_start: 0.6182 (OUTLIER) cc_final: 0.5738 (mt) REVERT: D 552 PHE cc_start: 0.7436 (m-10) cc_final: 0.7008 (m-10) outliers start: 34 outliers final: 21 residues processed: 137 average time/residue: 0.1045 time to fit residues: 21.5023 Evaluate side-chains 128 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 126 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106561 restraints weight = 19329.675| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3328 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11687 Z= 0.141 Angle : 0.521 7.199 15739 Z= 0.276 Chirality : 0.041 0.155 1688 Planarity : 0.004 0.069 2005 Dihedral : 4.572 23.791 1511 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.75 % Allowed : 22.15 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.02 (0.23), residues: 1362 helix: 1.08 (0.19), residues: 721 sheet: -0.37 (0.57), residues: 95 loop : -1.35 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 369 TYR 0.018 0.001 TYR B 347 PHE 0.012 0.001 PHE D 308 TRP 0.006 0.001 TRP A1223 HIS 0.003 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00314 (11672) covalent geometry : angle 0.51689 (15730) hydrogen bonds : bond 0.04696 ( 531) hydrogen bonds : angle 4.36843 ( 1521) metal coordination : bond 0.00521 ( 15) metal coordination : angle 2.82989 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 818 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: A 1016 TYR cc_start: 0.7661 (t80) cc_final: 0.7459 (t80) REVERT: A 1288 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5945 (mm) REVERT: B 213 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: B 238 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7952 (mt) REVERT: D 312 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5632 (mt) REVERT: D 552 PHE cc_start: 0.7429 (m-10) cc_final: 0.7059 (m-10) outliers start: 35 outliers final: 24 residues processed: 140 average time/residue: 0.1084 time to fit residues: 22.6034 Evaluate side-chains 130 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 23 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.129439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.106491 restraints weight = 19371.658| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.95 r_work: 0.3327 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11687 Z= 0.141 Angle : 0.520 6.539 15739 Z= 0.276 Chirality : 0.041 0.156 1688 Planarity : 0.004 0.072 2005 Dihedral : 4.578 23.865 1511 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.14 % Allowed : 22.07 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.02 (0.23), residues: 1362 helix: 1.08 (0.19), residues: 721 sheet: -0.40 (0.57), residues: 95 loop : -1.36 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 369 TYR 0.018 0.001 TYR B 347 PHE 0.012 0.001 PHE D 308 TRP 0.007 0.001 TRP B 261 HIS 0.003 0.001 HIS A 815 Details of bonding type rmsd covalent geometry : bond 0.00313 (11672) covalent geometry : angle 0.51537 (15730) hydrogen bonds : bond 0.04695 ( 531) hydrogen bonds : angle 4.36140 ( 1521) metal coordination : bond 0.00518 ( 15) metal coordination : angle 2.82117 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 818 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8011 (m-30) REVERT: A 1288 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5973 (mm) REVERT: B 213 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: B 238 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7946 (mt) REVERT: D 312 ILE cc_start: 0.5989 (OUTLIER) cc_final: 0.5623 (mt) REVERT: D 552 PHE cc_start: 0.7440 (m-10) cc_final: 0.7081 (m-10) outliers start: 40 outliers final: 27 residues processed: 138 average time/residue: 0.1046 time to fit residues: 21.9839 Evaluate side-chains 133 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 101 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 470 SER Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 41 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 131 optimal weight: 0.0870 chunk 87 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 126 optimal weight: 0.2980 chunk 98 optimal weight: 0.0020 chunk 130 optimal weight: 3.9990 overall best weight: 0.2966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN C 275 GLN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.132211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.109279 restraints weight = 19178.606| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.86 r_work: 0.3389 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11687 Z= 0.095 Angle : 0.466 5.576 15739 Z= 0.249 Chirality : 0.039 0.154 1688 Planarity : 0.004 0.069 2005 Dihedral : 4.242 22.715 1511 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 2.44 % Allowed : 22.70 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.35 (0.23), residues: 1362 helix: 1.40 (0.19), residues: 707 sheet: -0.21 (0.58), residues: 94 loop : -1.22 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 369 TYR 0.012 0.001 TYR B 347 PHE 0.013 0.001 PHE A 995 TRP 0.006 0.001 TRP A 775 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00187 (11672) covalent geometry : angle 0.46359 (15730) hydrogen bonds : bond 0.04025 ( 531) hydrogen bonds : angle 4.15874 ( 1521) metal coordination : bond 0.00388 ( 15) metal coordination : angle 2.13016 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.501 Fit side-chains revert: symmetry clash REVERT: A 818 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: A 1288 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5910 (mm) REVERT: B 213 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: D 312 ILE cc_start: 0.6006 (OUTLIER) cc_final: 0.5589 (mp) REVERT: D 495 GLN cc_start: 0.7304 (mt0) cc_final: 0.7069 (mt0) REVERT: D 552 PHE cc_start: 0.7412 (m-10) cc_final: 0.6930 (m-10) outliers start: 31 outliers final: 21 residues processed: 141 average time/residue: 0.0996 time to fit residues: 21.2453 Evaluate side-chains 129 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 86 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 72 optimal weight: 0.1980 chunk 69 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 118 optimal weight: 0.0030 chunk 68 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 88 optimal weight: 0.0050 chunk 111 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.2804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN D 519 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.133328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110434 restraints weight = 19050.924| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.87 r_work: 0.3407 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11687 Z= 0.091 Angle : 0.457 6.162 15739 Z= 0.243 Chirality : 0.039 0.160 1688 Planarity : 0.004 0.069 2005 Dihedral : 4.064 20.725 1511 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.36 % Allowed : 23.02 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.54 (0.23), residues: 1362 helix: 1.50 (0.20), residues: 707 sheet: 0.14 (0.59), residues: 90 loop : -1.10 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 369 TYR 0.013 0.001 TYR B 347 PHE 0.012 0.001 PHE A 995 TRP 0.007 0.001 TRP B 261 HIS 0.004 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00181 (11672) covalent geometry : angle 0.45440 (15730) hydrogen bonds : bond 0.03800 ( 531) hydrogen bonds : angle 4.06403 ( 1521) metal coordination : bond 0.00401 ( 15) metal coordination : angle 2.03554 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 719 TRP cc_start: 0.6463 (t60) cc_final: 0.5883 (t60) REVERT: A 818 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: A 1288 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5856 (mm) REVERT: B 213 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: C 360 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7727 (mt-10) REVERT: D 312 ILE cc_start: 0.5984 (OUTLIER) cc_final: 0.5561 (mp) REVERT: D 495 GLN cc_start: 0.7220 (mt0) cc_final: 0.6991 (mt0) REVERT: D 552 PHE cc_start: 0.7336 (m-10) cc_final: 0.6954 (m-10) outliers start: 30 outliers final: 21 residues processed: 144 average time/residue: 0.0937 time to fit residues: 20.5859 Evaluate side-chains 137 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 76 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 129 optimal weight: 0.0870 chunk 64 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1274 ASN ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108155 restraints weight = 19252.636| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.88 r_work: 0.3372 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11687 Z= 0.118 Angle : 0.494 6.250 15739 Z= 0.262 Chirality : 0.040 0.154 1688 Planarity : 0.004 0.069 2005 Dihedral : 4.224 21.746 1511 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.28 % Allowed : 22.94 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.48 (0.23), residues: 1362 helix: 1.44 (0.20), residues: 707 sheet: 0.08 (0.59), residues: 90 loop : -1.10 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1273 TYR 0.016 0.001 TYR B 347 PHE 0.021 0.001 PHE A 720 TRP 0.006 0.001 TRP B 261 HIS 0.003 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00256 (11672) covalent geometry : angle 0.49070 (15730) hydrogen bonds : bond 0.04199 ( 531) hydrogen bonds : angle 4.16007 ( 1521) metal coordination : bond 0.00504 ( 15) metal coordination : angle 2.55308 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2724 Ramachandran restraints generated. 1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 719 TRP cc_start: 0.6487 (t60) cc_final: 0.5877 (t60) REVERT: A 818 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: A 1288 LEU cc_start: 0.6280 (OUTLIER) cc_final: 0.5973 (mm) REVERT: B 213 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: C 373 TYR cc_start: 0.7933 (m-10) cc_final: 0.7707 (m-80) REVERT: D 312 ILE cc_start: 0.6118 (OUTLIER) cc_final: 0.5656 (mt) REVERT: D 552 PHE cc_start: 0.7412 (m-10) cc_final: 0.6977 (m-10) outliers start: 29 outliers final: 23 residues processed: 137 average time/residue: 0.1006 time to fit residues: 20.9265 Evaluate side-chains 133 residues out of total 1273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 774 CYS Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 1199 VAL Chi-restraints excluded: chain A residue 1256 LEU Chi-restraints excluded: chain A residue 1266 MET Chi-restraints excluded: chain A residue 1288 LEU Chi-restraints excluded: chain A residue 1313 SER Chi-restraints excluded: chain A residue 1320 ASP Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 180 ASN Chi-restraints excluded: chain D residue 278 CYS Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 312 ILE Chi-restraints excluded: chain D residue 318 THR Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 343 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 562 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 5 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 GLN D 342 ASN ** D 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.131211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108032 restraints weight = 19213.181| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.97 r_work: 0.3364 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11687 Z= 0.114 Angle : 0.493 6.192 15739 Z= 0.261 Chirality : 0.040 0.198 1688 Planarity : 0.004 0.071 2005 Dihedral : 4.245 21.901 1511 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.59 % Allowed : 22.86 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: 0.44 (0.23), residues: 1362 helix: 1.38 (0.19), residues: 713 sheet: 0.11 (0.59), residues: 90 loop : -1.11 (0.27), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1273 TYR 0.016 0.001 TYR B 347 PHE 0.020 0.001 PHE A 720 TRP 0.006 0.001 TRP A1223 HIS 0.002 0.001 HIS A 998 Details of bonding type rmsd covalent geometry : bond 0.00245 (11672) covalent geometry : angle 0.48980 (15730) hydrogen bonds : bond 0.04210 ( 531) hydrogen bonds : angle 4.16715 ( 1521) metal coordination : bond 0.00467 ( 15) metal coordination : angle 2.52064 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.26 seconds wall clock time: 54 minutes 23.12 seconds (3263.12 seconds total)