Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 04:24:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi2_33849/10_2023/7yi2_33849.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi2_33849/10_2023/7yi2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi2_33849/10_2023/7yi2_33849.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi2_33849/10_2023/7yi2_33849.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi2_33849/10_2023/7yi2_33849.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi2_33849/10_2023/7yi2_33849.pdb" } 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 Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 695": "OD1" <-> "OD2" Residue "A PHE 720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 762": "OD1" <-> "OD2" Residue "A GLU 874": "OE1" <-> "OE2" Residue "A ASP 902": "OD1" <-> "OD2" Residue "A GLU 904": "OE1" <-> "OE2" Residue "A GLU 911": "OE1" <-> "OE2" Residue "A PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1160": "OE1" <-> "OE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "C ASP 251": "OD1" <-> "OD2" Residue "C ASP 361": "OD1" <-> "OD2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D GLU 323": "OE1" <-> "OE2" Residue "D ASP 553": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 6.66, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 1.8 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: 4.28 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: 4.04 Time building geometry restraints manager: 5.66 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: 99.10 - 106.10: 410 106.10 - 113.09: 6554 113.09 - 120.09: 4650 120.09 - 127.09: 5148 127.09 - 134.08: 187 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: 6743 26.50 - 53.00: 548 53.00 - 79.50: 79 79.50 - 106.00: 7 106.00 - 132.50: 1 Dihedral angle restraints: 7378 sinusoidal: 3261 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 7375 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 2.440 nonbonded pdb=" OG SER D 109 " pdb=" O LEU D 113 " model vdw 2.214 2.440 nonbonded pdb=" NE2 GLN D 510 " pdb=" O GLY D 513 " model vdw 2.224 2.520 nonbonded pdb=" O LYS D 321 " pdb=" OG SER D 324 " model vdw 2.232 2.440 ... (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 ========== 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: 1.350 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: 7.800 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 40.280 Find NCS groups from input model: 0.340 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: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.910 ------------------------------------------------------------------------------- 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 12469 Z= 0.193 Angle : 0.595 11.236 16949 Z= 0.342 Chirality : 0.039 0.140 1826 Planarity : 0.006 0.126 2046 Dihedral : 18.171 132.505 4716 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.494 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.3022 time to fit residues: 47.6221 Evaluate side-chains 101 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 1.422 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1106 time to fit residues: 2.0909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.0870 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 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: 2.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- 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 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 12469 Z= 0.409 Angle : 0.699 13.632 16949 Z= 0.372 Chirality : 0.045 0.180 1826 Planarity : 0.006 0.089 2046 Dihedral : 16.833 135.319 1840 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.17 % Favored : 89.76 % Rotamer: Outliers : 4.54 % Allowed : 19.33 % Favored : 76.13 % 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: -1.44 (0.22), residues: 1367 helix: 0.48 (0.19), residues: 681 sheet: -2.21 (0.49), residues: 104 loop : -2.51 (0.24), residues: 582 *********************** 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 158 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 100 time to evaluate : 1.534 Fit side-chains revert: symmetry clash outliers start: 58 outliers final: 37 residues processed: 148 average time/residue: 0.2652 time to fit residues: 56.5197 Evaluate side-chains 135 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 98 time to evaluate : 1.521 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1351 time to fit residues: 11.2165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 HIS ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12469 Z= 0.190 Angle : 0.545 9.716 16949 Z= 0.296 Chirality : 0.040 0.142 1826 Planarity : 0.005 0.067 2046 Dihedral : 16.640 136.848 1840 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.72 % Allowed : 21.13 % Favored : 77.15 % 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: -0.98 (0.23), residues: 1367 helix: 0.89 (0.20), residues: 679 sheet: -1.86 (0.51), residues: 104 loop : -2.36 (0.24), residues: 584 *********************** 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 133 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 131 average time/residue: 0.2757 time to fit residues: 51.6908 Evaluate side-chains 106 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.463 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1266 time to fit residues: 3.1006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 ASN ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12469 Z= 0.236 Angle : 0.572 10.940 16949 Z= 0.307 Chirality : 0.041 0.146 1826 Planarity : 0.005 0.061 2046 Dihedral : 16.695 138.409 1840 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 2.82 % Allowed : 21.67 % Favored : 75.51 % 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: -0.98 (0.23), residues: 1367 helix: 0.87 (0.20), residues: 680 sheet: -1.77 (0.51), residues: 104 loop : -2.35 (0.24), residues: 583 *********************** 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 139 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 103 time to evaluate : 1.662 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 23 residues processed: 134 average time/residue: 0.2535 time to fit residues: 49.9616 Evaluate side-chains 122 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 99 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1168 time to fit residues: 6.9551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 121 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS A 959 GLN ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 GLN ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12469 Z= 0.183 Angle : 0.536 9.375 16949 Z= 0.288 Chirality : 0.039 0.142 1826 Planarity : 0.004 0.056 2046 Dihedral : 16.607 138.661 1840 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.17 % Allowed : 22.54 % Favored : 76.29 % 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: -0.69 (0.23), residues: 1367 helix: 1.14 (0.20), residues: 674 sheet: -1.51 (0.52), residues: 99 loop : -2.25 (0.24), residues: 594 *********************** 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 124 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.470 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 121 average time/residue: 0.2942 time to fit residues: 51.3377 Evaluate side-chains 110 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 1.723 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1491 time to fit residues: 4.5037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- 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 ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12469 Z= 0.214 Angle : 0.552 9.668 16949 Z= 0.297 Chirality : 0.040 0.143 1826 Planarity : 0.004 0.056 2046 Dihedral : 16.630 138.697 1840 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.70 % Allowed : 23.40 % Favored : 75.90 % 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: -0.69 (0.23), residues: 1367 helix: 1.10 (0.20), residues: 679 sheet: -1.62 (0.51), residues: 104 loop : -2.20 (0.24), residues: 584 *********************** 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 111 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 111 average time/residue: 0.2661 time to fit residues: 42.7893 Evaluate side-chains 102 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1213 time to fit residues: 2.6596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 114 optimal weight: 0.0970 chunk 75 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 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 ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12469 Z= 0.148 Angle : 0.509 7.402 16949 Z= 0.276 Chirality : 0.039 0.156 1826 Planarity : 0.004 0.051 2046 Dihedral : 16.470 138.920 1840 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.70 % Allowed : 23.63 % Favored : 75.67 % 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: -0.42 (0.23), residues: 1367 helix: 1.36 (0.20), residues: 669 sheet: -1.33 (0.52), residues: 99 loop : -2.09 (0.24), residues: 599 *********************** 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 120 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 118 average time/residue: 0.2775 time to fit residues: 47.2720 Evaluate side-chains 106 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 104 time to evaluate : 1.505 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1146 time to fit residues: 2.5009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 122 optimal weight: 0.0570 chunk 129 optimal weight: 0.0020 overall best weight: 0.6308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12469 Z= 0.159 Angle : 0.515 7.956 16949 Z= 0.278 Chirality : 0.039 0.140 1826 Planarity : 0.004 0.052 2046 Dihedral : 16.434 139.311 1840 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 0.63 % Allowed : 24.10 % Favored : 75.27 % 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: -0.34 (0.23), residues: 1367 helix: 1.44 (0.20), residues: 667 sheet: -1.31 (0.52), residues: 99 loop : -2.05 (0.25), residues: 601 *********************** REFINEMENT MACRO_CYCLE 8 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 117 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 116 average time/residue: 0.2812 time to fit residues: 46.9819 Evaluate side-chains 112 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 105 time to evaluate : 1.435 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1198 time to fit residues: 3.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.8980 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.0770 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12469 Z= 0.160 Angle : 0.510 7.371 16949 Z= 0.277 Chirality : 0.039 0.148 1826 Planarity : 0.004 0.052 2046 Dihedral : 16.405 139.382 1840 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.08 % Allowed : 24.10 % Favored : 75.82 % 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: -0.29 (0.23), residues: 1367 helix: 1.48 (0.20), residues: 666 sheet: -1.24 (0.52), residues: 99 loop : -2.03 (0.25), residues: 602 *********************** REFINEMENT MACRO_CYCLE 9 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 105 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.2853 time to fit residues: 42.8009 Evaluate side-chains 102 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 785 HIS ** B 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 545 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12469 Z= 0.161 Angle : 0.515 7.422 16949 Z= 0.278 Chirality : 0.039 0.145 1826 Planarity : 0.004 0.052 2046 Dihedral : 16.387 139.385 1840 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.23 % Allowed : 24.10 % Favored : 75.67 % 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: -0.26 (0.23), residues: 1367 helix: 1.49 (0.20), residues: 668 sheet: -1.21 (0.53), residues: 99 loop : -2.01 (0.25), residues: 600 ********************** REFINEMENT MACRO_CYCLE 10 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 fitting. rotamer outliers: 3 poor density : 109 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 111 average time/residue: 0.2743 time to fit residues: 43.9406 Evaluate side-chains 104 residues out of total 1278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.431 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1144 time to fit residues: 2.1124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.579 > 50: distance: 110 - 139: 18.041 distance: 125 - 130: 22.526 distance: 130 - 131: 23.459 distance: 131 - 132: 19.611 distance: 131 - 134: 16.732 distance: 132 - 133: 11.613 distance: 132 - 136: 26.413 distance: 134 - 135: 31.616 distance: 136 - 137: 17.072 distance: 137 - 138: 8.367 distance: 137 - 140: 17.597 distance: 138 - 139: 10.200 distance: 138 - 147: 18.280 distance: 140 - 141: 17.386 distance: 141 - 142: 11.784 distance: 141 - 143: 14.023 distance: 142 - 144: 12.551 distance: 143 - 145: 14.750 distance: 144 - 146: 13.294 distance: 145 - 146: 18.805 distance: 147 - 148: 11.410 distance: 148 - 149: 11.929 distance: 148 - 151: 9.549 distance: 149 - 150: 11.942 distance: 149 - 157: 17.542 distance: 151 - 152: 3.497 distance: 152 - 153: 9.715 distance: 152 - 154: 33.727 distance: 153 - 155: 11.702 distance: 153 - 249: 18.468 distance: 154 - 156: 9.390 distance: 155 - 156: 31.108 distance: 157 - 158: 13.466 distance: 158 - 159: 5.143 distance: 158 - 161: 22.927 distance: 159 - 160: 17.685 distance: 159 - 168: 15.408 distance: 161 - 162: 13.570 distance: 162 - 163: 13.219 distance: 162 - 164: 3.471 distance: 163 - 165: 14.897 distance: 164 - 166: 9.155 distance: 165 - 167: 16.465 distance: 166 - 167: 14.117 distance: 168 - 169: 14.468 distance: 169 - 170: 33.322 distance: 169 - 172: 21.378 distance: 170 - 171: 23.483 distance: 170 - 176: 15.298 distance: 172 - 173: 35.462 distance: 173 - 174: 40.884 distance: 173 - 175: 22.353 distance: 176 - 177: 31.622 distance: 177 - 178: 27.243 distance: 177 - 180: 5.028 distance: 178 - 179: 30.388 distance: 178 - 182: 40.000 distance: 180 - 181: 26.114 distance: 181 - 249: 25.853 distance: 182 - 183: 12.319 distance: 183 - 184: 12.555 distance: 183 - 186: 6.162 distance: 184 - 185: 14.042 distance: 184 - 190: 26.469 distance: 186 - 187: 28.461 distance: 187 - 188: 38.990 distance: 187 - 189: 40.202 distance: 190 - 191: 19.487 distance: 191 - 192: 13.991 distance: 191 - 194: 6.819 distance: 192 - 193: 24.464 distance: 192 - 198: 5.987 distance: 195 - 196: 19.740 distance: 195 - 197: 6.861 distance: 198 - 199: 34.277 distance: 198 - 204: 13.711 distance: 199 - 200: 11.936 distance: 199 - 202: 25.030 distance: 200 - 201: 19.807 distance: 200 - 205: 26.438 distance: 202 - 203: 28.911 distance: 203 - 204: 33.601 distance: 205 - 206: 23.571 distance: 205 - 211: 22.535 distance: 206 - 207: 10.101 distance: 206 - 209: 16.181 distance: 207 - 208: 20.803 distance: 207 - 212: 11.785 distance: 209 - 210: 30.937 distance: 210 - 211: 20.869