Starting phenix.real_space_refine on Fri Jul 3 02:56:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rpx_24625/07_2026/7rpx_24625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpx_24625/07_2026/7rpx_24625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2026/7rpx_24625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2026/7rpx_24625.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2026/7rpx_24625.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2026/7rpx_24625.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2026/7rpx_24625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpx_24625/07_2026/7rpx_24625.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.022 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 Mn 3 7.51 5 P 62 5.49 5 S 32 5.16 5 C 7302 2.51 5 N 1944 2.21 5 O 2411 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11754 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1945 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain: "B" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "C" Number of atoms: 1926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1926 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 5, 'TRANS': 237} Chain: "X" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 637 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "Z" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 4687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4687 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 21, 'TRANS': 568} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.54, per 1000 atoms: 0.22 Number of scatterers: 11754 At special positions: 0 Unit cell: (114, 108, 120, 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) Mn 3 24.99 S 32 16.00 P 62 15.00 O 2411 8.00 N 1944 7.00 C 7302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 310.8 milliseconds 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2496 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 15 sheets defined 26.0% alpha, 19.4% beta 30 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 142 through 154 removed outlier: 4.351A pdb=" N LEU A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.973A pdb=" N SER B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 136 through 147 removed outlier: 4.263A pdb=" N ALA B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.502A pdb=" N ASN B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.445A pdb=" N ARG C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.877A pdb=" N SER C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 Processing helix chain 'C' and resid 204 through 211 removed outlier: 3.842A pdb=" N LEU C 207 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 208 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS C 209 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 21 through 30 removed outlier: 4.054A pdb=" N LEU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 42 removed outlier: 4.242A pdb=" N ASP E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.572A pdb=" N GLN E 46 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 77 through 89 removed outlier: 4.191A pdb=" N VAL E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 120 through 134 removed outlier: 3.508A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 153 removed outlier: 3.559A pdb=" N LEU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 168 removed outlier: 3.530A pdb=" N VAL E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 removed outlier: 3.677A pdb=" N VAL E 179 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 193 through 204 removed outlier: 4.203A pdb=" N LEU E 203 " --> pdb=" O ARG E 199 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 223 Processing helix chain 'E' and resid 289 through 297 removed outlier: 4.047A pdb=" N VAL E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP E 294 " --> pdb=" O PRO E 290 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 332 removed outlier: 4.015A pdb=" N ARG E 332 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 332' Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.631A pdb=" N ALA E 339 " --> pdb=" O ASP E 335 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 335 through 340' Processing helix chain 'E' and resid 392 through 398 removed outlier: 3.743A pdb=" N LYS E 397 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER E 398 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 404 Processing helix chain 'E' and resid 490 through 504 removed outlier: 3.764A pdb=" N GLN E 498 " --> pdb=" O LEU E 494 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS E 499 " --> pdb=" O ASP E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 574 Processing helix chain 'E' and resid 576 through 587 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.604A pdb=" N ILE A 4 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 110 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.527A pdb=" N ARG A 51 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 233 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 243 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 231 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 245 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 229 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY A 224 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 134 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 removed outlier: 4.155A pdb=" N MET A 157 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 179 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 170 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR A 177 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 178 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.011A pdb=" N LEU B 88 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.868A pdb=" N GLU B 66 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN B 26 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B 37 " --> pdb=" O ASN B 26 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 28 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 34 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 47 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 48 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP B 237 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 213 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 216 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 193 through 197 removed outlier: 3.681A pdb=" N ILE B 155 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 152 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 167 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 156 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 163 " --> pdb=" O HIS B 156 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 108 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 107 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 111 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 58 " --> pdb=" O VAL C 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.835A pdb=" N LYS C 28 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 165 Processing sheet with id=AB1, first strand: chain 'E' and resid 256 through 257 removed outlier: 3.601A pdb=" N VAL E 257 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 388 " --> pdb=" O VAL E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 265 through 266 removed outlier: 6.621A pdb=" N GLU E 308 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 312 " --> pdb=" O ASN E 346 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS E 383 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL E 347 " --> pdb=" O LYS E 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 354 through 355 removed outlier: 3.828A pdb=" N TYR E 355 " --> pdb=" O VAL E 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 505 through 506 removed outlier: 3.818A pdb=" N TRP E 522 " --> pdb=" O ARG E 506 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE E 521 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY E 453 " --> pdb=" O ILE E 521 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL E 451 " --> pdb=" O VAL E 523 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N LEU E 448 " --> pdb=" O TYR E 472 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N TYR E 472 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL E 450 " --> pdb=" O ALA E 470 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA E 470 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY E 452 " --> pdb=" O LEU E 468 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS E 483 " --> pdb=" O MET E 469 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ALA E 471 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER E 481 " --> pdb=" O ALA E 471 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN E 473 " --> pdb=" O PHE E 479 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE E 479 " --> pdb=" O ASN E 473 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE E 479 " --> pdb=" O ASN E 514 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 505 through 506 removed outlier: 3.818A pdb=" N TRP E 522 " --> pdb=" O ARG E 506 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE E 521 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY E 453 " --> pdb=" O ILE E 521 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL E 451 " --> pdb=" O VAL E 523 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 564 " --> pdb=" O GLU E 530 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE E 532 " --> pdb=" O PHE E 562 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N PHE E 562 " --> pdb=" O ILE E 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 536 through 539 311 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.19 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3508 1.34 - 1.46: 2187 1.46 - 1.58: 6196 1.58 - 1.70: 122 1.70 - 1.82: 61 Bond restraints: 12074 Sorted by residual: bond pdb=" C3' DT Z 30 " pdb=" C2' DT Z 30 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DC X 27 " pdb=" C2' DC X 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG X 9 " pdb=" C2' DG X 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG X 28 " pdb=" C2' DG X 28 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.64e+00 bond pdb=" C3' DT X 7 " pdb=" C2' DT X 7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 ... (remaining 12069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 16289 2.12 - 4.24: 245 4.24 - 6.37: 10 6.37 - 8.49: 1 8.49 - 10.61: 2 Bond angle restraints: 16547 Sorted by residual: angle pdb=" N3 DT Z 32 " pdb=" C4 DT Z 32 " pdb=" O4 DT Z 32 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" O4' DT X 23 " pdb=" C4' DT X 23 " pdb=" C3' DT X 23 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT X 26 " pdb=" C4 DT X 26 " pdb=" O4 DT X 26 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 angle pdb=" CA MET A 182 " pdb=" C MET A 182 " pdb=" O MET A 182 " ideal model delta sigma weight residual 121.47 116.61 4.86 1.15e+00 7.56e-01 1.79e+01 ... (remaining 16542 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.28: 6865 32.28 - 64.57: 335 64.57 - 96.85: 4 96.85 - 129.13: 0 129.13 - 161.42: 2 Dihedral angle restraints: 7206 sinusoidal: 3343 harmonic: 3863 Sorted by residual: dihedral pdb=" C4' DA Z 22 " pdb=" C3' DA Z 22 " pdb=" O3' DA Z 22 " pdb=" P DC Z 23 " ideal model delta sinusoidal sigma weight residual 220.00 58.58 161.42 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DA Z 16 " pdb=" C3' DA Z 16 " pdb=" O3' DA Z 16 " pdb=" P DG Z 17 " ideal model delta sinusoidal sigma weight residual 220.00 71.96 148.04 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CA PHE C 69 " pdb=" C PHE C 69 " pdb=" N ASN C 70 " pdb=" CA ASN C 70 " ideal model delta harmonic sigma weight residual 180.00 162.69 17.31 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 7203 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1719 0.081 - 0.161: 175 0.161 - 0.242: 1 0.242 - 0.323: 0 0.323 - 0.404: 1 Chirality restraints: 1896 Sorted by residual: chirality pdb=" P DG X 25 " pdb=" OP1 DG X 25 " pdb=" OP2 DG X 25 " pdb=" O5' DG X 25 " both_signs ideal model delta sigma weight residual True 2.34 -2.74 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA PRO A 186 " pdb=" N PRO A 186 " pdb=" C PRO A 186 " pdb=" CB PRO A 186 " both_signs ideal model delta sigma weight residual False 2.72 2.92 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C3' DA Z 22 " pdb=" C4' DA Z 22 " pdb=" O3' DA Z 22 " pdb=" C2' DA Z 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 ... (remaining 1893 not shown) Planarity restraints: 1892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 121 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO B 122 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 181 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C LEU A 181 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 181 " -0.011 2.00e-02 2.50e+03 pdb=" N MET A 182 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 226 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.22e+00 pdb=" N PRO E 227 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO E 227 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 227 " -0.021 5.00e-02 4.00e+02 ... (remaining 1889 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.30: 32 2.30 - 2.95: 5427 2.95 - 3.60: 17388 3.60 - 4.25: 26869 4.25 - 4.90: 42757 Nonbonded interactions: 92473 Sorted by model distance: nonbonded pdb=" O GLY E 60 " pdb="MN MN E 701 " model vdw 1.655 2.320 nonbonded pdb=" OP1 DG X 22 " pdb="MN MN X 101 " model vdw 1.753 2.320 nonbonded pdb=" O GLU E 167 " pdb="MN MN E 702 " model vdw 1.770 2.320 nonbonded pdb=" N GLY E 62 " pdb="MN MN E 701 " model vdw 1.887 2.400 nonbonded pdb=" C ILE E 61 " pdb="MN MN E 701 " model vdw 1.940 2.550 ... (remaining 92468 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.830 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12074 Z= 0.290 Angle : 0.600 10.609 16547 Z= 0.414 Chirality : 0.045 0.404 1896 Planarity : 0.003 0.051 1892 Dihedral : 15.951 161.418 4710 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.87 % Favored : 90.83 % Rotamer: Outliers : 0.86 % Allowed : 9.00 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.23), residues: 1319 helix: -0.91 (0.31), residues: 294 sheet: -0.63 (0.31), residues: 332 loop : -2.53 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 140 TYR 0.022 0.001 TYR C 200 PHE 0.014 0.001 PHE B 101 TRP 0.013 0.001 TRP E 431 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.29 (12074) covalent geometry : angle 0.59984 / 0.41 (16547) hydrogen bonds : bond 0.25909 / 16.42 ( 386) hydrogen bonds : angle 9.68139 / 6.57 ( 988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 294 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.7372 (t80) cc_final: 0.7114 (t80) REVERT: A 24 ASP cc_start: 0.6700 (t0) cc_final: 0.6025 (t0) REVERT: A 26 ILE cc_start: 0.8107 (pt) cc_final: 0.7892 (pt) REVERT: A 29 ASN cc_start: 0.6231 (m-40) cc_final: 0.5648 (m110) REVERT: A 30 PHE cc_start: 0.8159 (m-80) cc_final: 0.7948 (m-80) REVERT: A 69 LYS cc_start: 0.7697 (tppt) cc_final: 0.7478 (tppt) REVERT: A 86 LYS cc_start: 0.8023 (pttp) cc_final: 0.7302 (pptt) REVERT: A 164 ASP cc_start: 0.7677 (t0) cc_final: 0.5805 (t0) REVERT: A 182 MET cc_start: 0.4462 (mmm) cc_final: 0.4133 (mmm) REVERT: A 183 LYS cc_start: 0.8935 (tttt) cc_final: 0.8655 (mmtm) REVERT: A 210 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8308 (ptpt) REVERT: A 213 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.4581 (mpp80) REVERT: A 232 ASP cc_start: 0.6464 (t0) cc_final: 0.6008 (t0) REVERT: A 244 TRP cc_start: 0.7138 (m100) cc_final: 0.6772 (m100) REVERT: B 11 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.6350 (t80) REVERT: B 16 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7433 (ttm-80) REVERT: B 55 TYR cc_start: 0.4681 (OUTLIER) cc_final: 0.1758 (t80) REVERT: B 68 ILE cc_start: 0.8603 (mt) cc_final: 0.8102 (mm) REVERT: B 156 HIS cc_start: 0.6874 (p90) cc_final: 0.6504 (p-80) REVERT: B 191 ASP cc_start: 0.7241 (m-30) cc_final: 0.6496 (m-30) REVERT: C 70 ASN cc_start: 0.4626 (t0) cc_final: 0.4308 (t0) REVERT: C 83 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7832 (mpp80) REVERT: C 128 PHE cc_start: 0.6685 (m-80) cc_final: 0.4540 (m-10) REVERT: C 165 LYS cc_start: 0.6958 (pttp) cc_final: 0.6601 (pttp) REVERT: E 145 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4534 (ttm-80) REVERT: E 162 LEU cc_start: 0.7773 (mt) cc_final: 0.7260 (mt) REVERT: E 213 ILE cc_start: 0.8145 (mt) cc_final: 0.7722 (mt) REVERT: E 303 LYS cc_start: 0.8829 (mptp) cc_final: 0.8519 (mmtm) REVERT: E 454 PHE cc_start: 0.5176 (m-80) cc_final: 0.3306 (m-80) REVERT: E 517 MET cc_start: 0.5501 (ttm) cc_final: 0.5163 (ttm) REVERT: E 583 MET cc_start: 0.8854 (mtp) cc_final: 0.8507 (mtp) outliers start: 10 outliers final: 2 residues processed: 302 average time/residue: 0.1355 time to fit residues: 54.3273 Evaluate side-chains 222 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 216 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN E 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.188721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.159470 restraints weight = 23985.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.164078 restraints weight = 14763.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.167358 restraints weight = 10136.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.169818 restraints weight = 7547.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.171529 restraints weight = 5945.315| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4389 r_free = 0.4389 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4388 r_free = 0.4388 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.4388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12074 Z= 0.196 Angle : 0.763 8.972 16547 Z= 0.415 Chirality : 0.051 0.315 1896 Planarity : 0.005 0.054 1892 Dihedral : 19.553 161.148 2087 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.93 % Favored : 89.76 % Rotamer: Outliers : 0.09 % Allowed : 4.46 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.22), residues: 1319 helix: -1.21 (0.29), residues: 297 sheet: -0.95 (0.28), residues: 345 loop : -2.65 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 213 TYR 0.036 0.003 TYR B 13 PHE 0.035 0.003 PHE E 400 TRP 0.014 0.002 TRP E 50 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (12074) covalent geometry : angle 0.76336 / 0.41 (16547) hydrogen bonds : bond 0.06373 / 4.02 ( 386) hydrogen bonds : angle 7.72592 / 5.31 ( 988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.6462 (t0) cc_final: 0.5756 (t0) REVERT: A 76 LYS cc_start: 0.7548 (tptp) cc_final: 0.7347 (tptp) REVERT: A 89 ILE cc_start: 0.7714 (tt) cc_final: 0.7506 (tt) REVERT: A 124 GLN cc_start: 0.6959 (tm-30) cc_final: 0.6717 (tm-30) REVERT: A 163 GLU cc_start: 0.8167 (tp30) cc_final: 0.7871 (mm-30) REVERT: A 164 ASP cc_start: 0.7734 (t0) cc_final: 0.6001 (t0) REVERT: A 165 LYS cc_start: 0.8290 (pttm) cc_final: 0.8050 (pttm) REVERT: A 182 MET cc_start: 0.4136 (mmm) cc_final: 0.3913 (mmm) REVERT: A 183 LYS cc_start: 0.9095 (tttt) cc_final: 0.8869 (mmtm) REVERT: A 184 ASP cc_start: 0.7203 (t0) cc_final: 0.6763 (t0) REVERT: A 210 LYS cc_start: 0.8801 (ptmt) cc_final: 0.8051 (ptpp) REVERT: A 233 VAL cc_start: 0.4738 (p) cc_final: 0.4425 (p) REVERT: A 244 TRP cc_start: 0.7137 (m100) cc_final: 0.6714 (m100) REVERT: B 1 MET cc_start: 0.5182 (ttm) cc_final: 0.4549 (tpp) REVERT: B 16 ARG cc_start: 0.7814 (mtm180) cc_final: 0.7540 (ttm-80) REVERT: B 59 PHE cc_start: 0.7468 (t80) cc_final: 0.7153 (t80) REVERT: B 156 HIS cc_start: 0.6941 (p90) cc_final: 0.6469 (p-80) REVERT: B 206 LYS cc_start: 0.8282 (ttmt) cc_final: 0.8032 (ttmm) REVERT: C 2 LYS cc_start: 0.7973 (tptp) cc_final: 0.7765 (tppt) REVERT: C 78 LEU cc_start: 0.7789 (mt) cc_final: 0.7549 (mt) REVERT: C 110 ASN cc_start: 0.7599 (t0) cc_final: 0.7381 (t0) REVERT: C 230 MET cc_start: 0.0421 (mtp) cc_final: 0.0083 (mtp) REVERT: E 143 LYS cc_start: 0.7527 (mttt) cc_final: 0.7270 (mtpp) REVERT: E 160 LYS cc_start: 0.7468 (mttt) cc_final: 0.7022 (ptpp) REVERT: E 166 VAL cc_start: 0.8877 (t) cc_final: 0.8623 (p) REVERT: E 180 LEU cc_start: 0.7412 (mt) cc_final: 0.7185 (mt) REVERT: E 213 ILE cc_start: 0.8148 (mt) cc_final: 0.7831 (mt) REVERT: E 229 VAL cc_start: 0.7440 (t) cc_final: 0.7218 (p) REVERT: E 288 GLN cc_start: 0.7691 (mt0) cc_final: 0.7013 (mp10) REVERT: E 303 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8665 (mmtm) REVERT: E 338 GLU cc_start: 0.7188 (tp30) cc_final: 0.6716 (tp30) REVERT: E 583 MET cc_start: 0.8747 (mtp) cc_final: 0.8495 (mtp) outliers start: 1 outliers final: 0 residues processed: 241 average time/residue: 0.1325 time to fit residues: 42.5410 Evaluate side-chains 203 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 36 optimal weight: 0.8980 chunk 101 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.188455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.159860 restraints weight = 24150.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.164422 restraints weight = 14853.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.167582 restraints weight = 10168.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.169963 restraints weight = 7584.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.171614 restraints weight = 5984.767| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4392 r_free = 0.4392 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4392 r_free = 0.4392 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12074 Z= 0.158 Angle : 0.687 9.638 16547 Z= 0.372 Chirality : 0.048 0.248 1896 Planarity : 0.005 0.054 1892 Dihedral : 19.606 162.293 2087 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.93 % Favored : 89.84 % Rotamer: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.22), residues: 1319 helix: -1.32 (0.28), residues: 303 sheet: -1.13 (0.29), residues: 323 loop : -2.67 (0.21), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 112 TYR 0.021 0.002 TYR B 13 PHE 0.030 0.002 PHE B 27 TRP 0.011 0.002 TRP E 431 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (12074) covalent geometry : angle 0.68703 / 0.37 (16547) hydrogen bonds : bond 0.05180 / 3.27 ( 386) hydrogen bonds : angle 7.08537 / 4.85 ( 988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.6902 (t0) cc_final: 0.6174 (t0) REVERT: A 163 GLU cc_start: 0.8119 (tp30) cc_final: 0.7850 (mm-30) REVERT: A 164 ASP cc_start: 0.7760 (t0) cc_final: 0.6129 (t0) REVERT: A 165 LYS cc_start: 0.8483 (pttm) cc_final: 0.8074 (pttm) REVERT: A 183 LYS cc_start: 0.9132 (tttt) cc_final: 0.8838 (mmtm) REVERT: A 184 ASP cc_start: 0.7479 (t0) cc_final: 0.7098 (t0) REVERT: A 185 LYS cc_start: 0.8025 (mmmt) cc_final: 0.7816 (mmmt) REVERT: A 244 TRP cc_start: 0.7097 (m100) cc_final: 0.6762 (m100) REVERT: B 28 ILE cc_start: 0.5021 (OUTLIER) cc_final: 0.4494 (mp) REVERT: B 59 PHE cc_start: 0.7494 (t80) cc_final: 0.7235 (t80) REVERT: B 156 HIS cc_start: 0.6852 (p90) cc_final: 0.6392 (p-80) REVERT: B 196 TYR cc_start: 0.7024 (m-80) cc_final: 0.6529 (m-10) REVERT: B 199 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 206 LYS cc_start: 0.8305 (ttmt) cc_final: 0.8019 (ttmm) REVERT: B 218 PHE cc_start: 0.8465 (t80) cc_final: 0.6955 (t80) REVERT: C 78 LEU cc_start: 0.7883 (mt) cc_final: 0.7660 (mt) REVERT: C 112 ARG cc_start: 0.7386 (ptm-80) cc_final: 0.6867 (ptm-80) REVERT: C 143 ILE cc_start: 0.6314 (tt) cc_final: 0.5987 (tt) REVERT: E 54 LEU cc_start: 0.8803 (mm) cc_final: 0.8452 (mt) REVERT: E 99 LYS cc_start: 0.8147 (tttt) cc_final: 0.7825 (tttt) REVERT: E 166 VAL cc_start: 0.8883 (t) cc_final: 0.8653 (p) REVERT: E 180 LEU cc_start: 0.7482 (mt) cc_final: 0.7239 (mt) REVERT: E 213 ILE cc_start: 0.8109 (mt) cc_final: 0.7811 (mt) REVERT: E 229 VAL cc_start: 0.7434 (t) cc_final: 0.7179 (t) REVERT: E 258 ASP cc_start: 0.7082 (p0) cc_final: 0.6703 (p0) REVERT: E 259 TYR cc_start: 0.6760 (m-10) cc_final: 0.6128 (m-80) REVERT: E 288 GLN cc_start: 0.7818 (mt0) cc_final: 0.7178 (mp10) REVERT: E 303 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8703 (mmtm) REVERT: E 338 GLU cc_start: 0.6995 (tp30) cc_final: 0.6545 (tp30) REVERT: E 342 GLU cc_start: 0.7569 (tp30) cc_final: 0.7071 (tp30) REVERT: E 517 MET cc_start: 0.6398 (tmm) cc_final: 0.5824 (tmm) REVERT: E 583 MET cc_start: 0.8723 (mtp) cc_final: 0.8471 (mtp) outliers start: 2 outliers final: 0 residues processed: 244 average time/residue: 0.1224 time to fit residues: 39.6303 Evaluate side-chains 204 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 203 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 122 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 133 optimal weight: 50.0000 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 0.0570 chunk 96 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 0.0470 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.190169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.161288 restraints weight = 23859.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.165967 restraints weight = 14603.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.169282 restraints weight = 9919.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.171664 restraints weight = 7307.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.173308 restraints weight = 5745.702| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4411 r_free = 0.4411 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4411 r_free = 0.4411 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.3516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12074 Z= 0.143 Angle : 0.669 9.940 16547 Z= 0.362 Chirality : 0.047 0.279 1896 Planarity : 0.004 0.055 1892 Dihedral : 19.632 162.899 2087 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.39 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.21), residues: 1319 helix: -1.41 (0.28), residues: 311 sheet: -1.18 (0.29), residues: 326 loop : -2.72 (0.21), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.020 0.002 TYR C 73 PHE 0.030 0.002 PHE B 27 TRP 0.013 0.002 TRP A 244 HIS 0.002 0.000 HIS E 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (12074) covalent geometry : angle 0.66917 / 0.36 (16547) hydrogen bonds : bond 0.04525 / 2.86 ( 386) hydrogen bonds : angle 6.70813 / 4.62 ( 988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7041 (t0) cc_final: 0.6305 (t0) REVERT: A 29 ASN cc_start: 0.6163 (m110) cc_final: 0.5226 (m110) REVERT: A 78 ILE cc_start: 0.8590 (mm) cc_final: 0.8100 (tp) REVERT: A 163 GLU cc_start: 0.8166 (tp30) cc_final: 0.7893 (mm-30) REVERT: A 164 ASP cc_start: 0.7754 (t0) cc_final: 0.6246 (t0) REVERT: A 165 LYS cc_start: 0.8475 (pttm) cc_final: 0.8169 (pttm) REVERT: A 183 LYS cc_start: 0.9119 (tttt) cc_final: 0.8795 (mmtm) REVERT: A 185 LYS cc_start: 0.8050 (mmmt) cc_final: 0.7780 (mmmt) REVERT: B 59 PHE cc_start: 0.7523 (t80) cc_final: 0.7270 (t80) REVERT: B 145 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6590 (mm-30) REVERT: B 156 HIS cc_start: 0.6736 (p90) cc_final: 0.6297 (p-80) REVERT: B 158 LYS cc_start: 0.8052 (tptp) cc_final: 0.7748 (tppt) REVERT: B 196 TYR cc_start: 0.6989 (m-80) cc_final: 0.6279 (m-10) REVERT: B 199 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7366 (tm-30) REVERT: B 218 PHE cc_start: 0.8228 (t80) cc_final: 0.6576 (t80) REVERT: B 225 LYS cc_start: 0.6752 (tttm) cc_final: 0.6434 (tttm) REVERT: C 78 LEU cc_start: 0.7831 (mt) cc_final: 0.7564 (mt) REVERT: C 79 LYS cc_start: 0.7739 (pttt) cc_final: 0.7515 (pttm) REVERT: C 112 ARG cc_start: 0.7318 (ptm-80) cc_final: 0.6722 (ptm-80) REVERT: C 187 GLU cc_start: 0.6519 (tm-30) cc_final: 0.5967 (tm-30) REVERT: E 53 PHE cc_start: 0.6583 (p90) cc_final: 0.6345 (p90) REVERT: E 54 LEU cc_start: 0.8554 (mm) cc_final: 0.8146 (mt) REVERT: E 99 LYS cc_start: 0.8162 (tttt) cc_final: 0.7853 (tttt) REVERT: E 166 VAL cc_start: 0.8884 (t) cc_final: 0.8490 (p) REVERT: E 180 LEU cc_start: 0.7515 (mt) cc_final: 0.7270 (mt) REVERT: E 213 ILE cc_start: 0.8031 (mt) cc_final: 0.7759 (mt) REVERT: E 229 VAL cc_start: 0.7466 (t) cc_final: 0.7189 (t) REVERT: E 258 ASP cc_start: 0.7176 (p0) cc_final: 0.6675 (p0) REVERT: E 259 TYR cc_start: 0.6644 (m-10) cc_final: 0.6039 (m-80) REVERT: E 288 GLN cc_start: 0.7763 (mt0) cc_final: 0.7508 (mt0) REVERT: E 303 LYS cc_start: 0.8952 (mmtm) cc_final: 0.8716 (mmtm) REVERT: E 338 GLU cc_start: 0.6944 (tp30) cc_final: 0.6699 (tp30) REVERT: E 342 GLU cc_start: 0.7578 (tp30) cc_final: 0.7142 (tp30) REVERT: E 414 LYS cc_start: 0.7282 (mmmt) cc_final: 0.6794 (mmtm) REVERT: E 583 MET cc_start: 0.8708 (mtp) cc_final: 0.8451 (mtp) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1261 time to fit residues: 39.3151 Evaluate side-chains 198 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 89 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.188314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.159504 restraints weight = 23736.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.164169 restraints weight = 14315.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.167443 restraints weight = 9683.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.169783 restraints weight = 7157.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.171462 restraints weight = 5655.036| |-----------------------------------------------------------------------------| r_work (final): 0.4386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4387 r_free = 0.4387 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4387 r_free = 0.4387 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12074 Z= 0.157 Angle : 0.667 10.583 16547 Z= 0.359 Chirality : 0.047 0.312 1896 Planarity : 0.004 0.061 1892 Dihedral : 19.588 163.962 2087 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.61 % Favored : 89.08 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.22), residues: 1319 helix: -1.32 (0.29), residues: 302 sheet: -1.23 (0.28), residues: 339 loop : -2.69 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 83 TYR 0.020 0.002 TYR C 200 PHE 0.028 0.002 PHE C 128 TRP 0.017 0.002 TRP E 431 HIS 0.002 0.001 HIS E 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (12074) covalent geometry : angle 0.66650 / 0.36 (16547) hydrogen bonds : bond 0.04480 / 2.82 ( 386) hydrogen bonds : angle 6.50572 / 4.49 ( 988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2638 Ramachandran restraints generated. 1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7120 (t0) cc_final: 0.6431 (t0) REVERT: A 29 ASN cc_start: 0.6177 (m110) cc_final: 0.5086 (m110) REVERT: A 76 LYS cc_start: 0.7373 (tptp) cc_final: 0.7131 (tptp) REVERT: A 78 ILE cc_start: 0.8662 (mm) cc_final: 0.8205 (tp) REVERT: A 165 LYS cc_start: 0.8619 (pttm) cc_final: 0.8259 (pttm) REVERT: A 210 LYS cc_start: 0.8799 (ptmt) cc_final: 0.8046 (ptpt) REVERT: B 59 PHE cc_start: 0.7512 (t80) cc_final: 0.7216 (t80) REVERT: B 145 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6729 (mm-30) REVERT: B 156 HIS cc_start: 0.6803 (p90) cc_final: 0.6353 (p-80) REVERT: B 158 LYS cc_start: 0.8049 (tptp) cc_final: 0.7737 (tppt) REVERT: B 199 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7204 (tm-30) REVERT: C 78 LEU cc_start: 0.7886 (mt) cc_final: 0.7581 (mt) REVERT: C 79 LYS cc_start: 0.7711 (pttt) cc_final: 0.7377 (pttm) REVERT: C 112 ARG cc_start: 0.7370 (ptm-80) cc_final: 0.6822 (ptm-80) REVERT: C 187 GLU cc_start: 0.6403 (tm-30) cc_final: 0.5860 (tm-30) REVERT: E 54 LEU cc_start: 0.8472 (mm) cc_final: 0.8205 (mt) REVERT: E 66 LEU cc_start: 0.7688 (mt) cc_final: 0.7401 (mm) REVERT: E 99 LYS cc_start: 0.8215 (tttt) cc_final: 0.7923 (tttt) REVERT: E 166 VAL cc_start: 0.9056 (t) cc_final: 0.8825 (p) REVERT: E 180 LEU cc_start: 0.7628 (mt) cc_final: 0.7406 (mt) REVERT: E 213 ILE cc_start: 0.8067 (mt) cc_final: 0.7794 (mt) REVERT: E 258 ASP cc_start: 0.7188 (p0) cc_final: 0.6633 (p0) REVERT: E 259 TYR cc_start: 0.6605 (m-10) cc_final: 0.5822 (m-80) REVERT: E 288 GLN cc_start: 0.7758 (mt0) cc_final: 0.7541 (mt0) REVERT: E 304 GLU cc_start: 0.7388 (pm20) cc_final: 0.7060 (pm20) REVERT: E 338 GLU cc_start: 0.7065 (tp30) cc_final: 0.6806 (tp30) REVERT: E 342 GLU cc_start: 0.7640 (tp30) cc_final: 0.7277 (tp30) REVERT: E 343 TYR cc_start: 0.6913 (m-80) cc_final: 0.6560 (m-10) REVERT: E 414 LYS cc_start: 0.7475 (mmmt) cc_final: 0.6862 (mmtm) REVERT: E 583 MET cc_start: 0.8698 (mtp) cc_final: 0.8456 (mtp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1275 time to fit residues: 38.8327 Evaluate side-chains 187 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 63.7329 > 50: distance: 29 - 142: 31.990 distance: 32 - 139: 29.513 distance: 55 - 74: 32.707 distance: 69 - 74: 30.147 distance: 74 - 75: 37.693 distance: 75 - 76: 30.515 distance: 75 - 78: 26.776 distance: 76 - 77: 32.418 distance: 76 - 83: 26.263 distance: 78 - 79: 20.953 distance: 79 - 80: 12.754 distance: 80 - 81: 3.141 distance: 81 - 82: 9.248 distance: 83 - 84: 15.197 distance: 84 - 85: 35.846 distance: 85 - 86: 59.040 distance: 85 - 87: 37.092 distance: 87 - 88: 44.145 distance: 88 - 89: 32.598 distance: 88 - 91: 21.962 distance: 89 - 90: 29.876 distance: 89 - 95: 13.589 distance: 91 - 92: 27.867 distance: 92 - 93: 26.183 distance: 92 - 94: 15.705 distance: 95 - 96: 25.058 distance: 96 - 97: 13.217 distance: 96 - 99: 27.785 distance: 97 - 98: 29.693 distance: 97 - 106: 14.624 distance: 99 - 100: 20.946 distance: 100 - 101: 10.646 distance: 106 - 107: 29.299 distance: 107 - 108: 34.669 distance: 108 - 109: 28.949 distance: 108 - 110: 34.210 distance: 110 - 111: 36.597 distance: 111 - 112: 20.991 distance: 111 - 114: 19.736 distance: 112 - 113: 43.257 distance: 112 - 121: 29.713 distance: 114 - 115: 19.973 distance: 115 - 116: 21.104 distance: 115 - 117: 20.285 distance: 116 - 118: 18.596 distance: 117 - 119: 19.311 distance: 118 - 120: 9.085 distance: 119 - 120: 11.850 distance: 121 - 122: 50.181 distance: 122 - 123: 47.356 distance: 122 - 125: 35.689 distance: 123 - 124: 16.492 distance: 123 - 127: 15.230 distance: 125 - 126: 20.707 distance: 127 - 128: 13.381 distance: 128 - 129: 22.189 distance: 128 - 131: 57.029 distance: 129 - 130: 35.580 distance: 129 - 132: 29.050 distance: 132 - 133: 47.089 distance: 132 - 138: 25.837 distance: 133 - 134: 35.786 distance: 133 - 136: 34.897 distance: 134 - 135: 41.564 distance: 134 - 139: 13.962 distance: 136 - 137: 30.110 distance: 137 - 138: 12.405 distance: 139 - 140: 21.668 distance: 140 - 141: 37.587 distance: 140 - 143: 36.440 distance: 141 - 142: 51.330 distance: 141 - 146: 25.200 distance: 143 - 144: 30.596 distance: 143 - 145: 9.945