Starting phenix.real_space_refine on Tue Jun 10 22:42:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yi2_33849/06_2025/7yi2_33849.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yi2_33849/06_2025/7yi2_33849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yi2_33849/06_2025/7yi2_33849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yi2_33849/06_2025/7yi2_33849.map" model { file = "/net/cci-nas-00/data/ceres_data/7yi2_33849/06_2025/7yi2_33849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yi2_33849/06_2025/7yi2_33849.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Zn 5 6.06 5 P 33 5.49 5 S 66 5.16 5 C 7644 2.51 5 N 2051 2.21 5 O 2341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 12140 Number of models: 1 Model: "" Number of chains: 9 Chain: "G" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 347 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} 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: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2626 Classifications: {'peptide': 321} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 302} 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 9823 SG CYS D 263 45.192 98.283 35.197 1.00 82.35 S ATOM 9840 SG CYS D 266 47.386 95.169 34.847 1.00 75.72 S ATOM 9993 SG CYS D 286 48.607 98.051 37.042 1.00 87.95 S ATOM 9925 SG CYS D 278 37.477 107.248 31.247 1.00102.60 S ATOM 10151 SG CYS D 306 37.138 109.944 30.588 1.00 95.03 S ATOM 11072 SG CYS D 440 68.674 66.827 27.274 1.00 44.61 S ATOM 11098 SG CYS D 443 71.466 66.135 24.692 1.00 57.38 S ATOM 11287 SG CYS D 466 72.291 66.083 28.297 1.00 69.65 S ATOM 10884 SG CYS D 417 71.804 56.226 31.155 1.00 48.05 S ATOM 10911 SG CYS D 420 72.125 52.570 32.298 1.00 70.53 S ATOM 11167 SG CYS D 451 72.311 55.368 34.881 1.00 47.98 S Time building chain proxies: 8.16, per 1000 atoms: 0.67 Number of scatterers: 12140 At special positions: 0 Unit cell: (125.57, 139.643, 101.755, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 5 29.99 S 66 16.00 P 33 15.00 O 2341 8.00 N 2051 7.00 C 7644 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: 3.31 Conformation dependent library (CDL) restraints added in 1.5 seconds 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 283 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 263 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 286 " pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 278 " pdb="ZN ZN D 702 " - pdb=" SG CYS D 306 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 469 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 466 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 443 " pdb="ZN ZN D 703 " - pdb=" SG CYS D 440 " pdb=" ZN D 704 " pdb="ZN ZN D 704 " - pdb=" ND1 HIS D 448 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 420 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 451 " pdb="ZN ZN D 704 " - pdb=" SG CYS D 417 " Number of angles added : 9 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2662 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 53.6% alpha, 6.0% beta 15 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 667 through 677 Processing helix chain 'A' and resid 679 through 694 Processing helix chain 'A' and resid 699 through 711 Processing helix chain 'A' and resid 715 through 725 Processing helix chain 'A' and resid 759 through 764 removed outlier: 3.733A pdb=" N PHE A 764 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 785 through 790 removed outlier: 3.799A pdb=" N ALA A 789 " --> pdb=" O HIS A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 839 removed outlier: 3.590A pdb=" N LYS A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.639A pdb=" N ASP A 881 " --> pdb=" O PHE A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 921 Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 930 through 935 removed outlier: 3.840A pdb=" N THR A 934 " --> pdb=" O HIS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 943 removed outlier: 3.811A pdb=" N LYS A 941 " --> pdb=" O GLN A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 960 removed outlier: 3.727A pdb=" N LEU A 948 " --> pdb=" O THR A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 999 removed outlier: 4.039A pdb=" N TYR A 986 " --> pdb=" O LYS A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1022 removed outlier: 4.180A pdb=" N GLU A1008 " --> pdb=" O ASN A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1031 Processing helix chain 'A' and resid 1141 through 1164 removed outlier: 3.993A 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 1181 through 1186 Processing helix chain 'A' and resid 1202 through 1217 Processing helix chain 'A' and resid 1220 through 1233 removed outlier: 3.524A pdb=" N PHE A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1240 removed outlier: 3.698A pdb=" N LEU A1239 " --> pdb=" O ALA A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1258 Processing helix chain 'A' and resid 1259 through 1276 removed outlier: 3.647A pdb=" N SER A1276 " --> pdb=" O ASP A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1294 removed outlier: 3.550A pdb=" N TYR A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 removed outlier: 3.875A pdb=" N ARG B 46 " --> pdb=" O PRO B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 removed outlier: 3.632A pdb=" N LYS B 59 " --> pdb=" O GLY B 56 " (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 98 through 105 removed outlier: 4.183A pdb=" N VAL B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 137 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.558A pdb=" N LEU B 168 " --> pdb=" O ASN B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.817A pdb=" N PHE B 197 " --> pdb=" O VAL B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 243 through 262 removed outlier: 3.995A pdb=" N SER B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) Proline residue: B 253 - end of helix Processing helix chain 'B' and resid 272 through 276 removed outlier: 4.003A pdb=" N SER B 275 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 300 removed outlier: 4.006A pdb=" N CYS B 294 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 295 " --> pdb=" O HIS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 330 removed outlier: 4.110A pdb=" N ARG B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 removed outlier: 4.155A 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: 3.630A pdb=" N GLN C 267 " --> pdb=" O HIS C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 297 removed outlier: 3.620A pdb=" N LEU C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C 279 " --> pdb=" O GLN C 275 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ASN C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 321 through 325 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 369 removed outlier: 3.661A pdb=" N LEU C 354 " --> pdb=" O GLN C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 168 through 173 removed outlier: 4.013A pdb=" N LEU D 171 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU D 173 " --> pdb=" O PHE D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 312 Processing helix chain 'D' and resid 317 through 328 Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 403 through 407 Processing helix chain 'D' and resid 430 through 434 removed outlier: 3.635A pdb=" N SER D 434 " --> pdb=" O PRO D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 564 removed outlier: 3.595A pdb=" N LYS D 548 " --> pdb=" O GLU D 544 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP D 553 " --> pdb=" O TYR D 549 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LYS D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN D 562 " --> pdb=" O SER D 558 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG D 564 " --> pdb=" O MET D 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 563 Processing sheet with id=AA1, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.085A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A1306 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 975 through 978 removed outlier: 4.085A pdb=" N HIS A1311 " --> pdb=" O ASP A1306 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP A1306 " --> pdb=" O HIS A1311 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 22 through 24 removed outlier: 6.414A pdb=" N TYR B 23 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA B 66 " --> pdb=" O TYR B 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 144 removed outlier: 7.349A pdb=" N VAL B 267 " --> pdb=" O MET B 306 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL B 308 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 269 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 181 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 180 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS B 206 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR B 182 " --> pdb=" O CYS B 206 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE B 208 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASP B 184 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N LYS B 210 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL B 234 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N THR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL B 236 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER B 207 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 238 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N HIS B 209 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'D' and resid 273 through 274 removed outlier: 3.683A pdb=" N PHE D 282 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 364 through 366 Processing sheet with id=AA8, first strand: chain 'D' and resid 473 through 476 Processing sheet with id=AA9, first strand: chain 'D' and resid 505 through 506 524 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3254 1.33 - 1.45: 2422 1.45 - 1.57: 6626 1.57 - 1.69: 67 1.69 - 1.81: 100 Bond restraints: 12469 Sorted by residual: bond pdb=" CB PRO D 297 " pdb=" CG PRO D 297 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.23e+00 bond pdb=" CB PRO C 319 " pdb=" CG PRO C 319 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.01e+00 bond pdb=" CB PRO D 119 " pdb=" CG PRO D 119 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.94e+00 bond pdb=" C HIS D 469 " pdb=" N SER D 470 " ideal model delta sigma weight residual 1.330 1.352 -0.022 1.47e-02 4.63e+03 2.29e+00 bond pdb=" CG1 ILE B 170 " pdb=" CD1 ILE B 170 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.07e+00 ... (remaining 12464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 16747 2.25 - 4.49: 178 4.49 - 6.74: 20 6.74 - 8.99: 3 8.99 - 11.24: 1 Bond angle restraints: 16949 Sorted by residual: angle pdb=" C ILE D 291 " pdb=" N ASP D 292 " pdb=" CA ASP D 292 " ideal model delta sigma weight residual 120.94 132.18 -11.24 1.90e+00 2.77e-01 3.50e+01 angle pdb=" CA PRO D 297 " pdb=" N PRO D 297 " pdb=" CD PRO D 297 " ideal model delta sigma weight residual 112.00 105.18 6.82 1.40e+00 5.10e-01 2.37e+01 angle pdb=" CA PRO D 119 " pdb=" N PRO D 119 " pdb=" CD PRO D 119 " ideal model delta sigma weight residual 112.00 105.18 6.82 1.40e+00 5.10e-01 2.37e+01 angle pdb=" N ASP A 695 " pdb=" CA ASP A 695 " pdb=" CB ASP A 695 " ideal model delta sigma weight residual 113.65 108.22 5.43 1.47e+00 4.63e-01 1.36e+01 angle pdb=" CA LYS D 328 " pdb=" CB LYS D 328 " pdb=" CG LYS D 328 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 ... (remaining 16944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.50: 6757 26.50 - 53.00: 566 53.00 - 79.50: 79 79.50 - 106.00: 7 106.00 - 132.50: 1 Dihedral angle restraints: 7410 sinusoidal: 3293 harmonic: 4117 Sorted by residual: dihedral pdb=" CA GLN D 541 " pdb=" C GLN D 541 " pdb=" N ILE D 542 " pdb=" CA ILE D 542 " ideal model delta harmonic sigma weight residual -180.00 -154.46 -25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE D 551 " pdb=" C PHE D 551 " pdb=" N PHE D 552 " pdb=" CA PHE D 552 " ideal model delta harmonic sigma weight residual -180.00 -157.48 -22.52 0 5.00e+00 4.00e-02 2.03e+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 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7407 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1047 0.028 - 0.056: 500 0.056 - 0.084: 194 0.084 - 0.112: 72 0.112 - 0.140: 13 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CA PRO A 786 " pdb=" N PRO A 786 " pdb=" C PRO A 786 " pdb=" CB PRO A 786 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA VAL D 108 " pdb=" N VAL D 108 " pdb=" C VAL D 108 " pdb=" CB VAL D 108 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA GLU B 252 " pdb=" N GLU B 252 " pdb=" C GLU B 252 " pdb=" CB GLU B 252 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 1823 not shown) Planarity restraints: 2046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 296 " 0.086 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO D 297 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO D 297 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO D 297 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 118 " 0.084 5.00e-02 4.00e+02 1.23e-01 2.41e+01 pdb=" N PRO D 119 " -0.212 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=" CB ASP A 695 " 0.016 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" CG ASP A 695 " -0.058 2.00e-02 2.50e+03 pdb=" OD1 ASP A 695 " 0.021 2.00e-02 2.50e+03 pdb=" OD2 ASP A 695 " 0.020 2.00e-02 2.50e+03 ... (remaining 2043 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 169 2.63 - 3.20: 10848 3.20 - 3.76: 19091 3.76 - 4.33: 26267 4.33 - 4.90: 41890 Nonbonded interactions: 98265 Sorted by model distance: nonbonded pdb=" OD2 ASP B 186 " pdb="ZN ZN B 501 " model vdw 2.062 2.230 nonbonded pdb=" O ILE C 342 " pdb=" OG1 THR C 345 " model vdw 2.171 3.040 nonbonded pdb=" OG SER D 109 " pdb=" O LEU D 113 " model vdw 2.214 3.040 nonbonded pdb=" NE2 GLN D 510 " pdb=" O GLY D 513 " model vdw 2.224 3.120 nonbonded pdb=" O LYS D 321 " pdb=" OG SER D 324 " model vdw 2.232 3.040 ... (remaining 98260 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: 1.590 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.230 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 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 0.090 12484 Z= 0.135 Angle : 0.596 11.236 16958 Z= 0.343 Chirality : 0.039 0.140 1826 Planarity : 0.006 0.126 2046 Dihedral : 18.253 132.505 4748 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.23 % Allowed : 20.34 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.23), residues: 1367 helix: 0.93 (0.21), residues: 645 sheet: -1.64 (0.57), residues: 87 loop : -2.30 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1151 HIS 0.004 0.001 HIS A 785 PHE 0.017 0.001 PHE A 668 TYR 0.016 0.001 TYR B 82 ARG 0.002 0.000 ARG A 868 Details of bonding type rmsd hydrogen bonds : bond 0.14249 ( 553) hydrogen bonds : angle 6.24707 ( 1572) metal coordination : bond 0.00386 ( 15) metal coordination : angle 2.14827 ( 9) covalent geometry : bond 0.00297 (12469) covalent geometry : angle 0.59458 (16949) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 1.463 Fit side-chains revert: symmetry clash REVERT: A 799 ARG cc_start: 0.6740 (mmm-85) cc_final: 0.5843 (tpp80) REVERT: A 913 ASN cc_start: 0.7249 (m110) cc_final: 0.6996 (m-40) REVERT: A 1156 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: D 438 MET cc_start: 0.7107 (tpt) cc_final: 0.6758 (tpt) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.2942 time to fit residues: 46.4013 Evaluate side-chains 103 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain C residue 349 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS C 275 GLN D 268 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN D 510 GLN D 541 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.121895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.094324 restraints weight = 23389.413| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.22 r_work: 0.3278 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 12484 Z= 0.302 Angle : 0.732 13.962 16958 Z= 0.388 Chirality : 0.046 0.182 1826 Planarity : 0.006 0.086 2046 Dihedral : 17.103 134.985 1877 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.80 % Favored : 90.12 % Rotamer: Outliers : 3.99 % Allowed : 19.48 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1367 helix: 0.46 (0.20), residues: 680 sheet: -2.06 (0.51), residues: 99 loop : -2.49 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1151 HIS 0.011 0.002 HIS B 150 PHE 0.027 0.003 PHE B 251 TYR 0.024 0.002 TYR B 313 ARG 0.005 0.001 ARG D 125 Details of bonding type rmsd hydrogen bonds : bond 0.06333 ( 553) hydrogen bonds : angle 5.16399 ( 1572) metal coordination : bond 0.01271 ( 15) metal coordination : angle 2.57220 ( 9) covalent geometry : bond 0.00699 (12469) covalent geometry : angle 0.72950 (16949) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 103 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5832 (mp0) REVERT: A 669 PHE cc_start: 0.7235 (m-80) cc_final: 0.6959 (t80) REVERT: A 695 ASP cc_start: 0.7056 (t0) cc_final: 0.6814 (t0) REVERT: A 1138 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7076 (tp) REVERT: A 1283 GLN cc_start: 0.7345 (mm110) cc_final: 0.6939 (tp40) REVERT: D 175 MET cc_start: 0.6982 (ttm) cc_final: 0.6637 (ttm) outliers start: 51 outliers final: 28 residues processed: 145 average time/residue: 0.2767 time to fit residues: 57.5150 Evaluate side-chains 128 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain A residue 1257 MET Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 288 MET Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 331 ASN Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 522 ILE Chi-restraints excluded: chain D residue 523 ILE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 72 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS C 369 HIS D 503 GLN D 541 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.125814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.098453 restraints weight = 23558.325| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.20 r_work: 0.3350 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12484 Z= 0.130 Angle : 0.547 9.143 16958 Z= 0.297 Chirality : 0.040 0.156 1826 Planarity : 0.005 0.064 2046 Dihedral : 16.783 136.624 1872 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 3.13 % Allowed : 20.42 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.23), residues: 1367 helix: 1.00 (0.20), residues: 675 sheet: -1.17 (0.58), residues: 82 loop : -2.40 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1151 HIS 0.005 0.001 HIS B 49 PHE 0.016 0.001 PHE A 669 TYR 0.012 0.001 TYR B 313 ARG 0.003 0.000 ARG D 496 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 553) hydrogen bonds : angle 4.49748 ( 1572) metal coordination : bond 0.00559 ( 15) metal coordination : angle 2.19942 ( 9) covalent geometry : bond 0.00278 (12469) covalent geometry : angle 0.54513 (16949) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 669 PHE cc_start: 0.7120 (m-80) cc_final: 0.6888 (t80) REVERT: A 695 ASP cc_start: 0.6895 (t0) cc_final: 0.6495 (t0) REVERT: B 259 MET cc_start: 0.8312 (mtt) cc_final: 0.8028 (mtt) REVERT: D 175 MET cc_start: 0.6848 (ttm) cc_final: 0.6534 (ttm) REVERT: D 410 ASN cc_start: 0.7459 (m110) cc_final: 0.7082 (m-40) REVERT: D 503 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6903 (tm130) outliers start: 40 outliers final: 20 residues processed: 142 average time/residue: 0.2767 time to fit residues: 57.6083 Evaluate side-chains 122 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 503 GLN Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.124522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.097467 restraints weight = 23194.292| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.16 r_work: 0.3326 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12484 Z= 0.174 Angle : 0.586 10.904 16958 Z= 0.314 Chirality : 0.041 0.150 1826 Planarity : 0.005 0.058 2046 Dihedral : 16.863 138.135 1872 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.91 % Allowed : 20.03 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.23), residues: 1367 helix: 0.96 (0.20), residues: 674 sheet: -1.37 (0.56), residues: 89 loop : -2.38 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1151 HIS 0.006 0.001 HIS A 785 PHE 0.017 0.002 PHE B 251 TYR 0.016 0.002 TYR B 313 ARG 0.003 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 553) hydrogen bonds : angle 4.52406 ( 1572) metal coordination : bond 0.00750 ( 15) metal coordination : angle 2.07900 ( 9) covalent geometry : bond 0.00391 (12469) covalent geometry : angle 0.58373 (16949) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 107 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 669 PHE cc_start: 0.7206 (m-80) cc_final: 0.6941 (t80) REVERT: A 695 ASP cc_start: 0.7102 (t0) cc_final: 0.6665 (t0) REVERT: A 920 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7645 (tt0) REVERT: B 344 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.5683 (t80) REVERT: D 175 MET cc_start: 0.6924 (ttm) cc_final: 0.6615 (ttm) REVERT: D 410 ASN cc_start: 0.7478 (m110) cc_final: 0.7155 (m-40) REVERT: D 503 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.7149 (tp40) outliers start: 50 outliers final: 32 residues processed: 150 average time/residue: 0.3186 time to fit residues: 72.2655 Evaluate side-chains 136 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 503 GLN Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 127 optimal weight: 8.9990 chunk 134 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS A 959 GLN D 503 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.126781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.099394 restraints weight = 23186.102| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.19 r_work: 0.3360 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12484 Z= 0.118 Angle : 0.529 8.376 16958 Z= 0.286 Chirality : 0.039 0.150 1826 Planarity : 0.004 0.051 2046 Dihedral : 16.712 138.693 1872 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.90 % Allowed : 21.13 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1367 helix: 1.28 (0.20), residues: 671 sheet: -1.10 (0.58), residues: 84 loop : -2.25 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1151 HIS 0.004 0.001 HIS B 49 PHE 0.010 0.001 PHE B 251 TYR 0.012 0.001 TYR B 313 ARG 0.002 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 553) hydrogen bonds : angle 4.26841 ( 1572) metal coordination : bond 0.00443 ( 15) metal coordination : angle 2.00401 ( 9) covalent geometry : bond 0.00249 (12469) covalent geometry : angle 0.52760 (16949) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 669 PHE cc_start: 0.7045 (m-80) cc_final: 0.6817 (t80) REVERT: A 695 ASP cc_start: 0.7008 (t0) cc_final: 0.6620 (t0) REVERT: A 773 MET cc_start: 0.6002 (ttt) cc_final: 0.5562 (ttt) REVERT: D 175 MET cc_start: 0.6875 (ttm) cc_final: 0.6539 (ttm) REVERT: D 410 ASN cc_start: 0.7424 (m110) cc_final: 0.7060 (m-40) outliers start: 37 outliers final: 26 residues processed: 145 average time/residue: 0.2932 time to fit residues: 62.4697 Evaluate side-chains 129 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 561 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 137 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS A 913 ASN ** C 350 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.126483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.099382 restraints weight = 23620.037| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.13 r_work: 0.3364 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12484 Z= 0.130 Angle : 0.541 8.977 16958 Z= 0.291 Chirality : 0.040 0.147 1826 Planarity : 0.004 0.054 2046 Dihedral : 16.660 139.090 1872 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.52 % Allowed : 20.89 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1367 helix: 1.35 (0.20), residues: 671 sheet: -1.22 (0.55), residues: 89 loop : -2.16 (0.24), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1151 HIS 0.004 0.001 HIS B 49 PHE 0.013 0.001 PHE B 251 TYR 0.017 0.001 TYR A1204 ARG 0.003 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04443 ( 553) hydrogen bonds : angle 4.21276 ( 1572) metal coordination : bond 0.00517 ( 15) metal coordination : angle 1.87329 ( 9) covalent geometry : bond 0.00284 (12469) covalent geometry : angle 0.53933 (16949) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 110 time to evaluate : 1.774 Fit side-chains revert: symmetry clash REVERT: A 665 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.6001 (mp0) REVERT: A 669 PHE cc_start: 0.7054 (m-80) cc_final: 0.6799 (t80) REVERT: A 695 ASP cc_start: 0.7118 (t0) cc_final: 0.6719 (t0) REVERT: A 913 ASN cc_start: 0.7168 (m-40) cc_final: 0.6736 (m-40) REVERT: A 920 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7635 (tt0) REVERT: A 1156 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7466 (tt0) REVERT: B 344 TYR cc_start: 0.6861 (OUTLIER) cc_final: 0.5668 (t80) REVERT: D 175 MET cc_start: 0.6917 (ttm) cc_final: 0.6553 (ttm) REVERT: D 410 ASN cc_start: 0.7453 (m110) cc_final: 0.7096 (m-40) outliers start: 45 outliers final: 33 residues processed: 150 average time/residue: 0.2937 time to fit residues: 67.5229 Evaluate side-chains 144 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** 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 = 0.3945 r_free = 0.3945 target = 0.126058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.098580 restraints weight = 23228.923| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.19 r_work: 0.3354 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12484 Z= 0.139 Angle : 0.549 9.271 16958 Z= 0.296 Chirality : 0.040 0.155 1826 Planarity : 0.004 0.055 2046 Dihedral : 16.631 138.931 1872 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.60 % Allowed : 21.21 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.23), residues: 1367 helix: 1.34 (0.20), residues: 670 sheet: -1.24 (0.54), residues: 89 loop : -2.15 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1151 HIS 0.004 0.001 HIS B 49 PHE 0.027 0.001 PHE A1305 TYR 0.014 0.001 TYR B 313 ARG 0.003 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 553) hydrogen bonds : angle 4.20009 ( 1572) metal coordination : bond 0.00545 ( 15) metal coordination : angle 1.90804 ( 9) covalent geometry : bond 0.00307 (12469) covalent geometry : angle 0.54739 (16949) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2734 Ramachandran restraints generated. 1367 Oldfield, 0 Emsley, 1367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 105 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5988 (mp0) REVERT: A 669 PHE cc_start: 0.7090 (m-80) cc_final: 0.6808 (t80) REVERT: A 695 ASP cc_start: 0.7133 (t0) cc_final: 0.6727 (t0) REVERT: A 1156 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7458 (tt0) REVERT: B 344 TYR cc_start: 0.6870 (OUTLIER) cc_final: 0.5666 (t80) REVERT: D 175 MET cc_start: 0.6915 (ttm) cc_final: 0.6652 (ttm) REVERT: D 410 ASN cc_start: 0.7457 (m110) cc_final: 0.7101 (m-40) REVERT: D 560 MET cc_start: 0.6875 (mmm) cc_final: 0.5979 (tpt) outliers start: 46 outliers final: 37 residues processed: 144 average time/residue: 0.2406 time to fit residues: 51.3699 Evaluate side-chains 144 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 104 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 802 GLN Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 818 ASP Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 923 VAL Chi-restraints excluded: chain A residue 973 SER Chi-restraints excluded: chain A residue 1003 SER Chi-restraints excluded: chain A residue 1156 GLU Chi-restraints excluded: chain A residue 1210 LEU Chi-restraints excluded: chain A residue 1304 GLU Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 214 PHE Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 300 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 277 THR Chi-restraints excluded: chain D residue 316 MET Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 425 LEU Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 MET Chi-restraints excluded: chain D residue 440 CYS Chi-restraints excluded: chain D residue 452 VAL Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain E residue 550 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.1577 > 50: distance: 18 - 45: 37.982 distance: 24 - 29: 34.634 distance: 25 - 53: 33.940 distance: 29 - 30: 39.204 distance: 29 - 35: 11.018 distance: 30 - 31: 46.973 distance: 30 - 33: 39.486 distance: 31 - 32: 43.702 distance: 31 - 36: 14.203 distance: 32 - 61: 38.032 distance: 33 - 34: 54.665 distance: 34 - 35: 58.154 distance: 36 - 37: 57.716 distance: 37 - 38: 56.315 distance: 37 - 40: 23.475 distance: 38 - 45: 55.888 distance: 40 - 41: 19.201 distance: 41 - 42: 40.748 distance: 42 - 43: 24.756 distance: 42 - 44: 5.063 distance: 45 - 46: 56.773 distance: 46 - 47: 7.637 distance: 46 - 49: 33.783 distance: 47 - 48: 18.707 distance: 47 - 53: 57.715 distance: 49 - 50: 48.334 distance: 50 - 51: 41.482 distance: 50 - 52: 57.018 distance: 53 - 54: 40.443 distance: 54 - 55: 26.266 distance: 54 - 57: 13.162 distance: 55 - 56: 41.659 distance: 55 - 61: 59.357 distance: 57 - 58: 51.983 distance: 57 - 59: 52.081 distance: 58 - 60: 57.089 distance: 61 - 62: 24.844 distance: 62 - 63: 48.250 distance: 62 - 65: 47.686 distance: 63 - 64: 39.264 distance: 63 - 67: 57.104 distance: 65 - 66: 56.239 distance: 68 - 71: 41.075 distance: 69 - 70: 26.112 distance: 69 - 73: 57.471 distance: 73 - 74: 13.432 distance: 74 - 75: 42.364 distance: 74 - 77: 44.588 distance: 75 - 76: 11.215 distance: 75 - 80: 12.343 distance: 77 - 78: 38.524 distance: 77 - 79: 26.975 distance: 80 - 81: 19.034 distance: 81 - 82: 49.581 distance: 81 - 84: 37.595 distance: 82 - 83: 8.959 distance: 82 - 87: 39.850 distance: 84 - 85: 56.057 distance: 84 - 86: 55.488 distance: 87 - 88: 41.303 distance: 88 - 89: 42.334 distance: 88 - 91: 19.878 distance: 89 - 90: 47.578 distance: 89 - 95: 35.157 distance: 91 - 92: 40.829 distance: 92 - 93: 49.167 distance: 93 - 94: 27.491 distance: 95 - 96: 4.423 distance: 97 - 98: 38.811 distance: 97 - 103: 35.380 distance: 99 - 100: 22.190 distance: 100 - 102: 46.230