Starting phenix.real_space_refine on Mon May 26 02:33:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qti_18650/05_2025/8qti_18650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qti_18650/05_2025/8qti_18650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qti_18650/05_2025/8qti_18650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qti_18650/05_2025/8qti_18650.map" model { file = "/net/cci-nas-00/data/ceres_data/8qti_18650/05_2025/8qti_18650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qti_18650/05_2025/8qti_18650.cif" } resolution = 3.09 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= 0.003 sd= 0.026 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 92 5.49 5 Mg 1 5.21 5 S 89 5.16 5 C 17151 2.51 5 N 4961 2.21 5 O 5562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27858 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1708 Classifications: {'peptide': 225} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 210} Chain: "B" Number of atoms: 1782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1782 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 219} Chain: "C" Number of atoms: 8602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8602 Classifications: {'peptide': 1110} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1050} Chain: "F" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2592 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 8, 'TRANS': 315} Chain: "O" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1034 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "D" Number of atoms: 9884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1264, 9884 Classifications: {'peptide': 1264} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1206} Chain breaks: 1 Chain: "E" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 595 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Chain: "J" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 782 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain breaks: 1 Chain: "P" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 876 Classifications: {'DNA': 43} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 22750 SG CYS D 890 35.758 60.543 61.393 1.00 26.77 S ATOM 23312 SG CYS D 967 38.484 62.913 62.562 1.00 20.71 S ATOM 23354 SG CYS D 974 36.240 61.173 65.091 1.00 21.24 S ATOM 23373 SG CYS D 977 38.764 59.199 63.275 1.00 22.30 S ATOM 16177 SG CYS D 60 38.943 126.343 79.058 1.00 41.72 S ATOM 16195 SG CYS D 62 40.303 129.719 78.021 1.00 44.79 S ATOM 16304 SG CYS D 75 37.514 128.267 76.058 1.00 46.07 S ATOM 16330 SG CYS D 78 40.917 126.840 75.670 1.00 41.65 S Time building chain proxies: 15.28, per 1000 atoms: 0.55 Number of scatterers: 27858 At special positions: 0 Unit cell: (130.875, 167.554, 157.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 89 16.00 P 92 15.00 Mg 1 11.99 O 5562 8.00 N 4961 7.00 C 17151 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: 7.50 Conformation dependent library (CDL) restraints added in 3.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " Number of angles added : 12 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6138 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 44 sheets defined 43.7% alpha, 17.1% beta 36 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 11.24 Creating SS restraints... Processing helix chain 'A' and resid 30 through 45 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.929A pdb=" N GLY A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.083A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 4.037A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.743A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.763A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 69 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 237 through 243 Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 279 through 292 removed outlier: 4.601A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 Processing helix chain 'C' and resid 325 through 342 removed outlier: 3.648A pdb=" N VAL C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 396 removed outlier: 3.502A pdb=" N GLN C 379 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.723A pdb=" N LEU C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 435 through 444 Processing helix chain 'C' and resid 455 through 459 removed outlier: 4.210A pdb=" N ALA C 459 " --> pdb=" O ARG C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 465 removed outlier: 3.907A pdb=" N ARG C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.936A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 630 removed outlier: 4.462A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 725 removed outlier: 3.928A pdb=" N ASP C 724 " --> pdb=" O ASN C 721 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 725 " --> pdb=" O TYR C 722 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 721 through 725' Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 770 through 774 removed outlier: 4.669A pdb=" N ASP C 774 " --> pdb=" O VAL C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 817 Processing helix chain 'C' and resid 891 through 895 Processing helix chain 'C' and resid 912 through 917 Processing helix chain 'C' and resid 919 through 933 removed outlier: 3.537A pdb=" N LEU C 923 " --> pdb=" O ILE C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 954 Processing helix chain 'C' and resid 972 through 982 Processing helix chain 'C' and resid 1027 through 1031 Processing helix chain 'C' and resid 1060 through 1071 Processing helix chain 'C' and resid 1072 through 1081 Processing helix chain 'C' and resid 1086 through 1100 removed outlier: 3.690A pdb=" N VAL C1091 " --> pdb=" O THR C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1120 removed outlier: 3.664A pdb=" N LYS C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.675A pdb=" N LEU F 159 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 174 removed outlier: 3.604A pdb=" N GLY F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 207 removed outlier: 3.536A pdb=" N GLU F 184 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU F 206 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS F 207 " --> pdb=" O GLU F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 246 removed outlier: 4.706A pdb=" N ARG F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N LEU F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 254 through 273 Processing helix chain 'F' and resid 280 through 301 removed outlier: 3.882A pdb=" N TYR F 284 " --> pdb=" O LYS F 280 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TRP F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 329 removed outlier: 3.710A pdb=" N VAL F 313 " --> pdb=" O HIS F 309 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN F 326 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 341 Processing helix chain 'F' and resid 344 through 355 Processing helix chain 'F' and resid 372 through 376 Processing helix chain 'F' and resid 384 through 405 removed outlier: 3.661A pdb=" N THR F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER F 400 " --> pdb=" O ASP F 396 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL F 401 " --> pdb=" O GLN F 397 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 402 " --> pdb=" O LEU F 398 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU F 403 " --> pdb=" O GLN F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 408 through 418 removed outlier: 4.210A pdb=" N VAL F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 Processing helix chain 'F' and resid 437 through 453 removed outlier: 3.626A pdb=" N ARG F 453 " --> pdb=" O MET F 449 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 459 Processing helix chain 'F' and resid 460 through 464 removed outlier: 4.220A pdb=" N ASP F 463 " --> pdb=" O VAL F 460 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR F 464 " --> pdb=" O LEU F 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 460 through 464' Processing helix chain 'D' and resid 16 through 23 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 84 through 90 removed outlier: 3.520A pdb=" N ARG D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 121 through 130 removed outlier: 3.532A pdb=" N LYS D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 Processing helix chain 'D' and resid 147 through 181 removed outlier: 3.907A pdb=" N LEU D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D 158 " --> pdb=" O GLU D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 228 removed outlier: 3.734A pdb=" N ARG D 194 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 257 through 267 removed outlier: 3.568A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 removed outlier: 3.931A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 304 removed outlier: 3.848A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA D 301 " --> pdb=" O LYS D 297 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE D 302 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.744A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 339 through 360 Processing helix chain 'D' and resid 363 through 383 Processing helix chain 'D' and resid 402 through 407 removed outlier: 3.624A pdb=" N LYS D 407 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 463 Proline residue: D 454 - end of helix Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 492 removed outlier: 4.215A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 525 through 527 No H-bonds generated for 'chain 'D' and resid 525 through 527' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 623 Processing helix chain 'D' and resid 643 through 651 Processing helix chain 'D' and resid 667 through 674 Processing helix chain 'D' and resid 688 through 703 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.555A pdb=" N VAL D 708 " --> pdb=" O PRO D 704 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG D 725 " --> pdb=" O TYR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 762 Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 Processing helix chain 'D' and resid 809 through 818 removed outlier: 3.505A pdb=" N THR D 813 " --> pdb=" O ASN D 809 " (cutoff:3.500A) Processing helix chain 'D' and resid 844 through 881 removed outlier: 3.767A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR D 866 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA D 867 " --> pdb=" O ALA D 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 955 removed outlier: 3.635A pdb=" N ILE D 948 " --> pdb=" O GLY D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 967 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 Processing helix chain 'D' and resid 1005 through 1009 Processing helix chain 'D' and resid 1028 through 1038 Processing helix chain 'D' and resid 1118 through 1126 Processing helix chain 'D' and resid 1127 through 1146 removed outlier: 3.547A pdb=" N GLN D1132 " --> pdb=" O PRO D1128 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D1146 " --> pdb=" O VAL D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 4.133A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1195 Processing helix chain 'D' and resid 1210 through 1217 Processing helix chain 'D' and resid 1220 through 1228 Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1250 through 1256 removed outlier: 3.740A pdb=" N ILE D1254 " --> pdb=" O LYS D1250 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'D' and resid 1276 through 1283 removed outlier: 3.551A pdb=" N ALA D1282 " --> pdb=" O GLU D1278 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 34 removed outlier: 3.525A pdb=" N ASN E 34 " --> pdb=" O GLY E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 46 through 66 Processing helix chain 'E' and resid 87 through 99 Processing helix chain 'J' and resid 80 through 87 Processing helix chain 'J' and resid 90 through 104 removed outlier: 4.200A pdb=" N LEU J 104 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 15 removed outlier: 6.474A pdb=" N ARG A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.986A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.986A pdb=" N TYR A 96 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 85 through 86 Processing sheet with id=AA5, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.512A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ASP B 190 " --> pdb=" O PRO B 25 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N THR B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 183 " --> pdb=" O THR B 187 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE B 189 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.542A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 141 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.608A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.639A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 132 " --> pdb=" O GLU C 137 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU C 137 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.639A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ALA C 122 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASP C 147 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU C 124 " --> pdb=" O MET C 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB6, first strand: chain 'C' and resid 367 through 370 Processing sheet with id=AB7, first strand: chain 'C' and resid 175 through 182 removed outlier: 4.578A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 removed outlier: 5.160A pdb=" N GLN C 518 " --> pdb=" O LYS C 509 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU C 511 " --> pdb=" O THR C 516 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 516 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 496 through 497 removed outlier: 3.531A pdb=" N VAL C 532 " --> pdb=" O ARG C 553 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.653A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 658 through 662 removed outlier: 7.074A pdb=" N TYR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL C 644 " --> pdb=" O TYR C 648 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR C 650 " --> pdb=" O GLU C 642 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 667 through 668 Processing sheet with id=AC5, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC6, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.548A pdb=" N ILE C 726 " --> pdb=" O LYS C 888 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N LEU C 890 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 728 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 740 through 751 removed outlier: 3.717A pdb=" N GLY C 840 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 865 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N VAL C 838 " --> pdb=" O ALA C 865 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N LYS C 867 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N GLY C 836 " --> pdb=" O LYS C 867 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 836 " --> pdb=" O VAL C 787 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AC9, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.707A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AD2, first strand: chain 'C' and resid 1034 through 1035 Processing sheet with id=AD3, first strand: chain 'C' and resid 1058 through 1059 Processing sheet with id=AD4, first strand: chain 'C' and resid 1127 through 1129 removed outlier: 3.872A pdb=" N GLU D 9 " --> pdb=" O LEU C1129 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 359 through 360 removed outlier: 5.996A pdb=" N ILE F 359 " --> pdb=" O THR D 337 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 24 through 27 removed outlier: 7.817A pdb=" N HIS D 94 " --> pdb=" O TYR D 25 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU D 27 " --> pdb=" O HIS D 94 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU D 96 " --> pdb=" O GLU D 27 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 97 " --> pdb=" O ASP D 315 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP D 315 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N ALA D 99 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 10.061A pdb=" N VAL D 313 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 6.940A pdb=" N THR D 253 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AE1, first strand: chain 'D' and resid 896 through 899 removed outlier: 4.722A pdb=" N THR D 923 " --> pdb=" O ARG D 962 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AE3, first strand: chain 'D' and resid 1044 through 1045 Processing sheet with id=AE4, first strand: chain 'D' and resid 1076 through 1082 removed outlier: 4.976A pdb=" N LYS D1080 " --> pdb=" O PHE D1063 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE D1063 " --> pdb=" O LYS D1080 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY D1052 " --> pdb=" O VAL D1106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 6.781A pdb=" N ALA D1203 " --> pdb=" O ILE D1169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1271 through 1275 removed outlier: 3.512A pdb=" N GLN D1272 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU E 102 " --> pdb=" O GLN D1274 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 27 through 29 Processing sheet with id=AE8, first strand: chain 'J' and resid 39 through 40 1219 hydrogen bonds defined for protein. 3423 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 88 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 14.75 Time building geometry restraints manager: 8.74 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: 8680 1.33 - 1.45: 3761 1.45 - 1.57: 15729 1.57 - 1.69: 182 1.69 - 1.81: 158 Bond restraints: 28510 Sorted by residual: bond pdb=" N ASP F 143 " pdb=" CA ASP F 143 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.11e+00 bond pdb=" N LEU B 2 " pdb=" CA LEU B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N LEU J 6 " pdb=" CA LEU J 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" N LEU A 2 " pdb=" CA LEU A 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N PHE D 6 " pdb=" CA PHE D 6 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 ... (remaining 28505 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 37635 1.11 - 2.23: 1043 2.23 - 3.34: 255 3.34 - 4.46: 58 4.46 - 5.57: 3 Bond angle restraints: 38994 Sorted by residual: angle pdb=" C3' DG P 10 " pdb=" C2' DG P 10 " pdb=" C1' DG P 10 " ideal model delta sigma weight residual 101.60 105.36 -3.76 1.50e+00 4.44e-01 6.29e+00 angle pdb=" C3' DC P 7 " pdb=" C2' DC P 7 " pdb=" C1' DC P 7 " ideal model delta sigma weight residual 101.60 105.35 -3.75 1.50e+00 4.44e-01 6.26e+00 angle pdb=" C4' DC O 41 " pdb=" O4' DC O 41 " pdb=" C1' DC O 41 " ideal model delta sigma weight residual 109.70 106.01 3.69 1.50e+00 4.44e-01 6.06e+00 angle pdb=" C3' DA P 35 " pdb=" C2' DA P 35 " pdb=" C1' DA P 35 " ideal model delta sigma weight residual 101.60 105.17 -3.57 1.50e+00 4.44e-01 5.67e+00 angle pdb=" C3' DA P 47 " pdb=" C2' DA P 47 " pdb=" C1' DA P 47 " ideal model delta sigma weight residual 101.60 105.07 -3.47 1.50e+00 4.44e-01 5.35e+00 ... (remaining 38989 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.09: 16481 33.09 - 66.17: 713 66.17 - 99.26: 38 99.26 - 132.35: 1 132.35 - 165.43: 1 Dihedral angle restraints: 17234 sinusoidal: 7701 harmonic: 9533 Sorted by residual: dihedral pdb=" CA ILE C1032 " pdb=" C ILE C1032 " pdb=" N HIS C1033 " pdb=" CA HIS C1033 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" C4' DA P 35 " pdb=" C3' DA P 35 " pdb=" O3' DA P 35 " pdb=" P DA P 36 " ideal model delta sinusoidal sigma weight residual 220.00 54.57 165.43 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA ASP C 298 " pdb=" C ASP C 298 " pdb=" N LEU C 299 " pdb=" CA LEU C 299 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 17231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2856 0.029 - 0.059: 963 0.059 - 0.088: 331 0.088 - 0.118: 242 0.118 - 0.147: 42 Chirality restraints: 4434 Sorted by residual: chirality pdb=" CA ASN C 498 " pdb=" N ASN C 498 " pdb=" C ASN C 498 " pdb=" CB ASN C 498 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.42e-01 chirality pdb=" CA ILE D 509 " pdb=" N ILE D 509 " pdb=" C ILE D 509 " pdb=" CB ILE D 509 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE F 306 " pdb=" N ILE F 306 " pdb=" C ILE F 306 " pdb=" CB ILE F 306 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 4431 not shown) Planarity restraints: 4808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 717 " -0.015 2.00e-02 2.50e+03 1.16e-02 3.38e+00 pdb=" CG TRP C 717 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP C 717 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 717 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 717 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 717 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 717 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 717 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 717 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 717 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 231 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ASN F 231 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN F 231 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS F 232 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 404 " -0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 405 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 405 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 405 " -0.024 5.00e-02 4.00e+02 ... (remaining 4805 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 102 2.52 - 3.12: 20736 3.12 - 3.71: 42093 3.71 - 4.31: 59786 4.31 - 4.90: 100305 Nonbonded interactions: 223022 Sorted by model distance: nonbonded pdb=" OG SER F 165 " pdb=" OE2 GLU D 376 " model vdw 1.928 3.040 nonbonded pdb=" OG1 THR B 74 " pdb=" OE2 GLU D 608 " model vdw 2.014 3.040 nonbonded pdb=" OG SER J 90 " pdb=" OE1 GLU J 93 " model vdw 2.045 3.040 nonbonded pdb=" OG1 THR C 226 " pdb=" OD2 ASP C 256 " model vdw 2.072 3.040 nonbonded pdb=" O PHE D 849 " pdb=" OG1 THR D 852 " model vdw 2.081 3.040 ... (remaining 223017 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 2 through 226) } 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=0.30 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: 3.510 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: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 78.500 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28518 Z= 0.112 Angle : 0.486 5.572 39006 Z= 0.274 Chirality : 0.040 0.147 4434 Planarity : 0.003 0.043 4808 Dihedral : 16.368 165.435 11096 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.04 % Allowed : 0.11 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: 0.91 (0.15), residues: 3309 helix: 1.86 (0.15), residues: 1279 sheet: 0.53 (0.27), residues: 365 loop : -0.35 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP C 717 HIS 0.004 0.001 HIS C 470 PHE 0.015 0.001 PHE D1063 TYR 0.009 0.001 TYR E 53 ARG 0.004 0.000 ARG D1232 Details of bonding type rmsd hydrogen bonds : bond 0.15582 ( 1288) hydrogen bonds : angle 5.57843 ( 3599) metal coordination : bond 0.03586 ( 8) metal coordination : angle 1.76225 ( 12) covalent geometry : bond 0.00227 (28510) covalent geometry : angle 0.48526 (38994) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 314 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 43 ARG cc_start: 0.7929 (mtt-85) cc_final: 0.7643 (mtt90) outliers start: 1 outliers final: 0 residues processed: 315 average time/residue: 0.5337 time to fit residues: 242.6454 Evaluate side-chains 186 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 2.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 286 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 137 optimal weight: 0.2980 chunk 265 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 307 optimal weight: 7.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN C 377 GLN F 326 GLN F 423 GLN D 304 GLN E 66 ASN E 97 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.068985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.049528 restraints weight = 76515.272| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.67 r_work: 0.2654 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 28518 Z= 0.348 Angle : 0.712 12.629 39006 Z= 0.376 Chirality : 0.049 0.225 4434 Planarity : 0.005 0.049 4808 Dihedral : 15.854 167.120 4668 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.71 % Allowed : 6.70 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: 0.40 (0.14), residues: 3309 helix: 1.47 (0.15), residues: 1282 sheet: 0.06 (0.26), residues: 394 loop : -0.64 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 717 HIS 0.007 0.002 HIS D 103 PHE 0.031 0.002 PHE C 364 TYR 0.019 0.002 TYR D 130 ARG 0.011 0.001 ARG D 206 Details of bonding type rmsd hydrogen bonds : bond 0.06176 ( 1288) hydrogen bonds : angle 4.64282 ( 3599) metal coordination : bond 0.01453 ( 8) metal coordination : angle 2.52166 ( 12) covalent geometry : bond 0.00836 (28510) covalent geometry : angle 0.71081 (38994) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 190 time to evaluate : 2.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.8515 (pm20) cc_final: 0.8053 (pm20) REVERT: B 17 ASN cc_start: 0.9142 (m-40) cc_final: 0.8419 (m-40) REVERT: C 652 MET cc_start: 0.8576 (tpp) cc_final: 0.8336 (tpp) REVERT: F 220 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: F 454 HIS cc_start: 0.8008 (t-90) cc_final: 0.7569 (t-170) REVERT: F 458 SER cc_start: 0.7862 (t) cc_final: 0.7435 (p) REVERT: J 35 ASP cc_start: 0.8828 (p0) cc_final: 0.8530 (p0) outliers start: 20 outliers final: 16 residues processed: 204 average time/residue: 0.4447 time to fit residues: 138.6460 Evaluate side-chains 184 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 320 THR Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1033 HIS Chi-restraints excluded: chain C residue 1054 PHE Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 753 ASP Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 1055 ARG Chi-restraints excluded: chain D residue 1173 SER Chi-restraints excluded: chain D residue 1174 THR Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain J residue 29 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 308 optimal weight: 6.9990 chunk 240 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 279 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 46 optimal weight: 0.0270 chunk 259 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 HIS C 377 GLN F 180 ASN F 423 GLN D 467 GLN D 888 HIS E 66 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.052699 restraints weight = 76030.824| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.63 r_work: 0.2723 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28518 Z= 0.130 Angle : 0.533 11.073 39006 Z= 0.286 Chirality : 0.041 0.137 4434 Planarity : 0.004 0.042 4808 Dihedral : 15.775 166.751 4668 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.96 % Allowed : 7.94 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: 0.67 (0.15), residues: 3309 helix: 1.76 (0.15), residues: 1289 sheet: 0.26 (0.26), residues: 397 loop : -0.57 (0.15), residues: 1623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1221 HIS 0.003 0.001 HIS D1151 PHE 0.015 0.001 PHE D1187 TYR 0.020 0.001 TYR F 196 ARG 0.008 0.000 ARG A 186 Details of bonding type rmsd hydrogen bonds : bond 0.04424 ( 1288) hydrogen bonds : angle 4.21216 ( 3599) metal coordination : bond 0.00470 ( 8) metal coordination : angle 1.85373 ( 12) covalent geometry : bond 0.00293 (28510) covalent geometry : angle 0.53219 (38994) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 2.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 ASP cc_start: 0.8290 (m-30) cc_final: 0.8057 (p0) REVERT: B 16 GLU cc_start: 0.8374 (pm20) cc_final: 0.8005 (pm20) REVERT: B 17 ASN cc_start: 0.9089 (m-40) cc_final: 0.8319 (m-40) REVERT: C 218 ASP cc_start: 0.8537 (t0) cc_final: 0.8248 (t0) REVERT: F 220 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7053 (mp10) REVERT: F 454 HIS cc_start: 0.7993 (t-90) cc_final: 0.7520 (t-170) REVERT: F 458 SER cc_start: 0.8007 (t) cc_final: 0.7594 (p) REVERT: D 1053 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7136 (tmm-80) REVERT: D 1054 VAL cc_start: 0.9192 (p) cc_final: 0.8690 (p) outliers start: 27 outliers final: 12 residues processed: 209 average time/residue: 0.4221 time to fit residues: 138.2274 Evaluate side-chains 182 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 2.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1033 HIS Chi-restraints excluded: chain C residue 1054 PHE Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 235 GLU Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain D residue 753 ASP Chi-restraints excluded: chain D residue 1055 ARG Chi-restraints excluded: chain D residue 1173 SER Chi-restraints excluded: chain D residue 1174 THR Chi-restraints excluded: chain E residue 84 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 321 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 123 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 278 optimal weight: 10.0000 chunk 236 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1053 GLN F 180 ASN F 423 GLN D 467 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.069538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.050193 restraints weight = 76905.637| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.68 r_work: 0.2674 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2679 r_free = 0.2679 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28518 Z= 0.220 Angle : 0.572 11.629 39006 Z= 0.305 Chirality : 0.043 0.152 4434 Planarity : 0.004 0.043 4808 Dihedral : 15.914 165.867 4668 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.42 % Allowed : 8.58 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: 0.58 (0.15), residues: 3309 helix: 1.66 (0.15), residues: 1290 sheet: 0.33 (0.27), residues: 384 loop : -0.64 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 54 HIS 0.004 0.001 HIS C 671 PHE 0.017 0.002 PHE D1187 TYR 0.025 0.002 TYR F 196 ARG 0.005 0.000 ARG D 67 Details of bonding type rmsd hydrogen bonds : bond 0.04943 ( 1288) hydrogen bonds : angle 4.25257 ( 3599) metal coordination : bond 0.00954 ( 8) metal coordination : angle 2.00275 ( 12) covalent geometry : bond 0.00529 (28510) covalent geometry : angle 0.57095 (38994) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6618 Ramachandran restraints generated. 3309 Oldfield, 0 Emsley, 3309 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7477 (m) REVERT: B 16 GLU cc_start: 0.8395 (pm20) cc_final: 0.8136 (pm20) REVERT: B 17 ASN cc_start: 0.9122 (m-40) cc_final: 0.8414 (m-40) REVERT: C 218 ASP cc_start: 0.8558 (t0) cc_final: 0.8246 (t0) REVERT: F 220 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: F 454 HIS cc_start: 0.7983 (t-90) cc_final: 0.7449 (t-170) REVERT: F 458 SER cc_start: 0.8116 (t) cc_final: 0.7715 (p) REVERT: D 1053 ARG cc_start: 0.7650 (ttp80) cc_final: 0.7355 (ttp80) REVERT: E 93 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8932 (mm) outliers start: 40 outliers final: 25 residues processed: 203 average time/residue: 0.4139 time to fit residues: 132.5627 Evaluate side-chains 189 residues out of total 2808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 223 GLN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 772 LEU Chi-restraints excluded: chain C residue 1022 LEU Chi-restraints excluded: chain C residue 1033 HIS Chi-restraints excluded: chain C residue 1054 PHE Chi-restraints excluded: chain F residue 220 GLN Chi-restraints excluded: chain F residue 235 GLU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 753 ASP Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 1055 ARG Chi-restraints excluded: chain D residue 1173 SER Chi-restraints excluded: chain D residue 1174 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain J residue 29 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 53.8684 > 50: distance: 49 - 51: 12.249 distance: 51 - 52: 4.111 distance: 52 - 53: 7.056 distance: 52 - 55: 9.761 distance: 53 - 54: 6.622 distance: 53 - 59: 8.131 distance: 54 - 79: 31.112 distance: 55 - 56: 20.387 distance: 56 - 57: 17.677 distance: 56 - 58: 10.056 distance: 59 - 60: 11.425 distance: 59 - 65: 12.418 distance: 60 - 61: 7.895 distance: 60 - 63: 10.622 distance: 61 - 62: 6.813 distance: 61 - 66: 3.518 distance: 62 - 87: 15.075 distance: 63 - 64: 12.483 distance: 64 - 65: 15.461 distance: 66 - 67: 3.835 distance: 67 - 68: 6.853 distance: 67 - 70: 16.397 distance: 68 - 69: 13.022 distance: 68 - 71: 13.035 distance: 69 - 92: 16.231 distance: 71 - 72: 4.931 distance: 72 - 73: 4.291 distance: 72 - 75: 5.439 distance: 73 - 74: 11.967 distance: 73 - 79: 6.642 distance: 74 - 100: 10.045 distance: 75 - 76: 5.251 distance: 75 - 77: 12.071 distance: 76 - 78: 18.358 distance: 79 - 80: 5.353 distance: 80 - 81: 8.785 distance: 80 - 83: 11.694 distance: 81 - 82: 15.013 distance: 81 - 87: 10.468 distance: 82 - 108: 25.561 distance: 83 - 84: 5.365 distance: 84 - 85: 6.137 distance: 87 - 88: 9.542 distance: 88 - 89: 10.817 distance: 88 - 91: 15.608 distance: 89 - 90: 12.566 distance: 89 - 92: 8.635 distance: 90 - 113: 30.537 distance: 92 - 93: 11.619 distance: 93 - 94: 10.024 distance: 93 - 96: 13.821 distance: 94 - 95: 14.912 distance: 94 - 100: 11.218 distance: 95 - 118: 11.437 distance: 97 - 98: 8.642 distance: 97 - 99: 4.002 distance: 100 - 101: 19.378 distance: 101 - 102: 22.778 distance: 101 - 104: 6.193 distance: 102 - 103: 10.300 distance: 102 - 108: 19.965 distance: 108 - 109: 21.947 distance: 109 - 110: 13.336 distance: 109 - 112: 11.430 distance: 110 - 111: 11.346 distance: 110 - 113: 9.286 distance: 113 - 114: 8.497 distance: 114 - 115: 21.757 distance: 114 - 117: 24.291 distance: 115 - 116: 17.900 distance: 115 - 118: 7.621