Starting phenix.real_space_refine on Fri Sep 11 21:30:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rpx_24625/09_2026/7rpx_24625.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpx_24625/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rpx_24625/09_2026/7rpx_24625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpx_24625/09_2026/7rpx_24625.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rpx_24625/09_2026/7rpx_24625.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rpx_24625/09_2026/7rpx_24625.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rpx_24625/09_2026/7rpx_24625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpx_24625/09_2026/7rpx_24625.cif" } 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-2.2.1-6174/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: 2.61, 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: 0.96 Conformation dependent library (CDL) restraints added in 496.2 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: 1.34 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: 2.16 Time building geometry restraints manager: 1.24 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: 0.460 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: 0.030 Set scattering table: 0.030 Process input model: 12.760 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.730 ------------------------------------------------------------------------------- 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= 0.291 Angle : 0.601 10.609 16547 Z= 0.415 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 0.60124 / 0.42 (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 : 0.417 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: A 12 PHE cc_start: 0.7372 (t80) cc_final: 0.7113 (t80) REVERT: A 24 ASP cc_start: 0.6700 (t0) cc_final: 0.6029 (t0) REVERT: A 26 ILE cc_start: 0.8107 (pt) cc_final: 0.7894 (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: 0.7949 (m-80) REVERT: A 69 LYS cc_start: 0.7697 (tppt) cc_final: 0.7480 (tppt) REVERT: A 86 LYS cc_start: 0.8023 (pttp) cc_final: 0.7300 (pptt) REVERT: A 164 ASP cc_start: 0.7677 (t0) cc_final: 0.5803 (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: 0.8656 (mmtm) REVERT: A 210 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8313 (ptpt) REVERT: A 213 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.4565 (mpp80) REVERT: A 232 ASP cc_start: 0.6464 (t0) cc_final: 0.6006 (t0) REVERT: A 244 TRP cc_start: 0.7138 (m100) cc_final: 0.6773 (m100) REVERT: B 11 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.6352 (t80) REVERT: B 16 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7431 (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: 0.6503 (p-80) REVERT: B 191 ASP cc_start: 0.7241 (m-30) cc_final: 0.6495 (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: 0.7835 (mpp80) REVERT: C 128 PHE cc_start: 0.6685 (m-80) cc_final: 0.4538 (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: 0.4535 (ttm-80) REVERT: E 162 LEU cc_start: 0.7773 (mt) cc_final: 0.7262 (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: 0.8520 (mmtm) REVERT: E 454 PHE cc_start: 0.5176 (m-80) cc_final: 0.3310 (m-80) REVERT: E 517 MET cc_start: 0.5501 (ttm) cc_final: 0.5138 (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: 0.1519 time to fit residues: 60.7204 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 : 0.469 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4583 r_free = 0.4583 target = 0.188628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.159412 restraints weight = 23923.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.164047 restraints weight = 14748.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.167338 restraints weight = 10109.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.169664 restraints weight = 7521.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.171462 restraints weight = 5968.414| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4388 r_free = 0.4388 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 = 0.4387 r_free = 0.4387 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.4387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6040 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12074 Z= 0.185 Angle : 0.754 9.504 16547 Z= 0.410 Chirality : 0.051 0.273 1896 Planarity : 0.005 0.061 1892 Dihedral : 19.542 160.610 2087 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.63 % Favored : 90.07 % Rotamer: Outliers : 0.09 % Allowed : 4.28 % Favored : 95.63 % 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: -2.73 (0.22), residues: 1319 helix: -1.19 (0.29), residues: 297 sheet: -0.94 (0.28), residues: 345 loop : -2.64 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 107 TYR 0.030 0.002 TYR B 13 PHE 0.034 0.002 PHE E 400 TRP 0.012 0.002 TRP E 50 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (12074) covalent geometry : angle 0.75352 / 0.41 (16547) hydrogen bonds : bond 0.06276 / 3.97 ( 386) hydrogen bonds : angle 7.71491 / 5.30 ( 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 239 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 0.437 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: 0.6600 (t0) cc_final: 0.5888 (t0) REVERT: A 89 ILE cc_start: 0.7721 (tt) cc_final: 0.7515 (tt) REVERT: A 124 GLN cc_start: 0.6962 (tm-30) cc_final: 0.6712 (tm-30) REVERT: A 163 GLU cc_start: 0.8156 (tp30) cc_final: 0.7892 (mm-30) REVERT: A 164 ASP cc_start: 0.7699 (t0) cc_final: 0.5956 (t0) REVERT: A 182 MET cc_start: 0.4085 (mmm) cc_final: 0.3882 (mmm) REVERT: A 183 LYS cc_start: 0.9092 (tttt) cc_final: 0.8873 (mmtm) REVERT: A 184 ASP cc_start: 0.7186 (t0) cc_final: 0.6752 (t0) REVERT: A 210 LYS cc_start: 0.8805 (ptmt) cc_final: 0.8064 (ptpp) REVERT: A 233 VAL cc_start: 0.4719 (p) cc_final: 0.4393 (p) REVERT: A 244 TRP cc_start: 0.7102 (m100) cc_final: 0.6693 (m100) REVERT: B 1 MET cc_start: 0.5137 (ttm) cc_final: 0.4528 (tpp) REVERT: B 16 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7544 (ttm-80) REVERT: B 59 PHE cc_start: 0.7454 (t80) cc_final: 0.7147 (t80) REVERT: B 156 HIS cc_start: 0.6954 (p90) cc_final: 0.6484 (p-80) REVERT: B 206 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8025 (ttmm) REVERT: C 78 LEU cc_start: 0.7793 (mt) cc_final: 0.7552 (mt) REVERT: C 143 ILE cc_start: 0.6154 (tt) cc_final: 0.5762 (tt) REVERT: E 143 LYS cc_start: 0.7494 (mttt) cc_final: 0.7284 (mtpp) REVERT: E 160 LYS cc_start: 0.7450 (mttt) cc_final: 0.7010 (ptpp) REVERT: E 166 VAL cc_start: 0.8859 (t) cc_final: 0.8611 (p) REVERT: E 180 LEU cc_start: 0.7399 (mt) cc_final: 0.7175 (mt) REVERT: E 213 ILE cc_start: 0.8121 (mt) cc_final: 0.7811 (mt) REVERT: E 288 GLN cc_start: 0.7671 (mt0) cc_final: 0.7000 (mp10) REVERT: E 303 LYS cc_start: 0.8877 (mmtm) cc_final: 0.8676 (mmtm) REVERT: E 338 GLU cc_start: 0.7164 (tp30) cc_final: 0.6699 (tp30) REVERT: E 583 MET cc_start: 0.8650 (mtp) cc_final: 0.8398 (mtp) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.1471 time to fit residues: 47.0949 Evaluate side-chains 206 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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: 1.9990 chunk 101 optimal weight: 0.0000 chunk 116 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- 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 = 0.4590 r_free = 0.4590 target = 0.188622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.159562 restraints weight = 24105.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.164206 restraints weight = 14623.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.167505 restraints weight = 9938.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 70)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.169902 restraints weight = 7316.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.171627 restraints weight = 5766.078| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4391 r_free = 0.4391 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4391 r_free = 0.4391 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: 0.4391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6060 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12074 Z= 0.163 Angle : 0.683 9.501 16547 Z= 0.371 Chirality : 0.048 0.270 1896 Planarity : 0.004 0.054 1892 Dihedral : 19.571 161.451 2087 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.70 % Favored : 90.07 % Rotamer: Outliers : 0.17 % Allowed : 3.43 % Favored : 96.40 % 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: -2.88 (0.22), residues: 1319 helix: -1.27 (0.28), residues: 303 sheet: -1.09 (0.30), residues: 312 loop : -2.67 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 35 TYR 0.020 0.002 TYR B 13 PHE 0.032 0.002 PHE B 27 TRP 0.012 0.002 TRP E 50 HIS 0.002 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (12074) covalent geometry : angle 0.68300 / 0.37 (16547) hydrogen bonds : bond 0.05266 / 3.32 ( 386) hydrogen bonds : angle 7.12559 / 4.88 ( 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 243 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 241 time to evaluate : 0.433 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: A 24 ASP cc_start: 0.6894 (t0) cc_final: 0.6161 (t0) REVERT: A 163 GLU cc_start: 0.8136 (tp30) cc_final: 0.7860 (mm-30) REVERT: A 164 ASP cc_start: 0.7744 (t0) cc_final: 0.6058 (t0) REVERT: A 165 LYS cc_start: 0.8688 (pttm) cc_final: 0.8260 (pttm) REVERT: A 182 MET cc_start: 0.3567 (mmm) cc_final: 0.3295 (mmm) REVERT: A 183 LYS cc_start: 0.9129 (tttt) cc_final: 0.8891 (mmtm) REVERT: A 184 ASP cc_start: 0.7508 (t0) cc_final: 0.7060 (t0) REVERT: A 185 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7796 (mmmm) REVERT: A 210 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8034 (ptpp) REVERT: A 233 VAL cc_start: 0.4456 (p) cc_final: 0.4124 (p) REVERT: A 244 TRP cc_start: 0.7119 (m100) cc_final: 0.6748 (m100) REVERT: B 16 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7604 (ttm-80) REVERT: B 28 ILE cc_start: 0.5154 (OUTLIER) cc_final: 0.4680 (mp) REVERT: B 59 PHE cc_start: 0.7497 (t80) cc_final: 0.7243 (t80) REVERT: B 156 HIS cc_start: 0.6846 (p90) cc_final: 0.6378 (p-80) REVERT: B 158 LYS cc_start: 0.8093 (tptp) cc_final: 0.7887 (tppt) REVERT: B 191 ASP cc_start: 0.7663 (m-30) cc_final: 0.7398 (m-30) REVERT: B 196 TYR cc_start: 0.7020 (m-80) cc_final: 0.6542 (m-10) REVERT: B 199 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7510 (tm-30) REVERT: B 206 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7989 (ttmm) REVERT: B 218 PHE cc_start: 0.8445 (t80) cc_final: 0.6949 (t80) REVERT: C 78 LEU cc_start: 0.7867 (mt) cc_final: 0.7640 (mt) REVERT: C 112 ARG cc_start: 0.7384 (ptm-80) cc_final: 0.6827 (ptm-80) REVERT: C 143 ILE cc_start: 0.6194 (tt) cc_final: 0.5872 (tt) REVERT: E 54 LEU cc_start: 0.8842 (mm) cc_final: 0.8491 (mt) REVERT: E 99 LYS cc_start: 0.8175 (tttt) cc_final: 0.7866 (tttt) REVERT: E 143 LYS cc_start: 0.7577 (mttt) cc_final: 0.7343 (mtpp) REVERT: E 166 VAL cc_start: 0.8856 (t) cc_final: 0.8596 (p) REVERT: E 180 LEU cc_start: 0.7492 (mt) cc_final: 0.7222 (mt) REVERT: E 213 ILE cc_start: 0.8136 (mt) cc_final: 0.7830 (mt) REVERT: E 258 ASP cc_start: 0.7123 (p0) cc_final: 0.6841 (p0) REVERT: E 259 TYR cc_start: 0.6558 (m-10) cc_final: 0.5973 (m-80) REVERT: E 288 GLN cc_start: 0.7841 (mt0) cc_final: 0.7209 (mp10) REVERT: E 303 LYS cc_start: 0.8925 (mmtm) cc_final: 0.8693 (mmtm) REVERT: E 338 GLU cc_start: 0.7028 (tp30) cc_final: 0.6591 (tp30) REVERT: E 342 GLU cc_start: 0.7607 (tp30) cc_final: 0.7168 (tp30) REVERT: E 583 MET cc_start: 0.8727 (mtp) cc_final: 0.8471 (mtp) outliers start: 2 outliers final: 0 residues processed: 243 average time/residue: 0.1542 time to fit residues: 49.7000 Evaluate side-chains 209 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 0.9990 chunk 123 optimal weight: 20.0000 chunk 122 optimal weight: 0.4980 chunk 101 optimal weight: 0.6980 chunk 133 optimal weight: 50.0000 chunk 32 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 0.2980 chunk 72 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 100 ASN ** 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 = 0.189175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.159985 restraints weight = 23949.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.164585 restraints weight = 14666.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.167758 restraints weight = 10025.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.170053 restraints weight = 7462.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.171750 restraints weight = 5920.570| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4391 r_free = 0.4391 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4391 r_free = 0.4391 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6051 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12074 Z= 0.147 Angle : 0.671 9.715 16547 Z= 0.364 Chirality : 0.047 0.280 1896 Planarity : 0.004 0.055 1892 Dihedral : 19.591 162.138 2087 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.31 % Favored : 89.46 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: -2.89 (0.22), residues: 1319 helix: -1.27 (0.28), residues: 305 sheet: -1.08 (0.30), residues: 307 loop : -2.68 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 35 TYR 0.019 0.002 TYR C 200 PHE 0.034 0.002 PHE B 27 TRP 0.013 0.002 TRP A 244 HIS 0.002 0.001 HIS E 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (12074) covalent geometry : angle 0.67059 / 0.36 (16547) hydrogen bonds : bond 0.04623 / 2.92 ( 386) hydrogen bonds : angle 6.78236 / 4.66 ( 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 237 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.412 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: A 12 PHE cc_start: 0.7495 (t80) cc_final: 0.7236 (t80) REVERT: A 24 ASP cc_start: 0.7081 (t0) cc_final: 0.6348 (t0) REVERT: A 29 ASN cc_start: 0.6203 (m110) cc_final: 0.5221 (m110) REVERT: A 78 ILE cc_start: 0.8617 (mm) cc_final: 0.8117 (tp) REVERT: A 114 TYR cc_start: 0.6565 (m-10) cc_final: 0.6333 (m-10) REVERT: A 124 GLN cc_start: 0.7077 (tm-30) cc_final: 0.6785 (tm-30) REVERT: A 163 GLU cc_start: 0.8195 (tp30) cc_final: 0.7902 (mm-30) REVERT: A 164 ASP cc_start: 0.7766 (t0) cc_final: 0.6014 (t0) REVERT: A 165 LYS cc_start: 0.8568 (pttm) cc_final: 0.8367 (pttm) REVERT: A 183 LYS cc_start: 0.9101 (tttt) cc_final: 0.8799 (mmtm) REVERT: A 185 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7803 (mmmt) REVERT: A 244 TRP cc_start: 0.7029 (m100) cc_final: 0.6588 (m100) REVERT: B 59 PHE cc_start: 0.7498 (t80) cc_final: 0.7286 (t80) REVERT: B 145 GLU cc_start: 0.6950 (mm-30) cc_final: 0.6577 (mm-30) REVERT: B 156 HIS cc_start: 0.6737 (p90) cc_final: 0.6310 (p-80) REVERT: B 158 LYS cc_start: 0.8062 (tptp) cc_final: 0.7842 (tppt) REVERT: B 196 TYR cc_start: 0.7025 (m-80) cc_final: 0.6373 (m-10) REVERT: B 199 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7369 (tm-30) REVERT: B 218 PHE cc_start: 0.8283 (t80) cc_final: 0.6630 (t80) REVERT: C 66 LYS cc_start: 0.7237 (tttt) cc_final: 0.6943 (tttm) REVERT: C 78 LEU cc_start: 0.7811 (mt) cc_final: 0.7557 (mt) REVERT: C 79 LYS cc_start: 0.7672 (pttt) cc_final: 0.7463 (pttm) REVERT: C 85 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6923 (mp0) REVERT: C 112 ARG cc_start: 0.7408 (ptm-80) cc_final: 0.6773 (ptm-80) REVERT: C 187 GLU cc_start: 0.7074 (tm-30) cc_final: 0.6318 (tm-30) REVERT: C 230 MET cc_start: -0.0000 (mtp) cc_final: -0.0317 (mtp) REVERT: E 54 LEU cc_start: 0.8531 (mm) cc_final: 0.8209 (mt) REVERT: E 99 LYS cc_start: 0.8190 (tttt) cc_final: 0.7881 (tttt) REVERT: E 143 LYS cc_start: 0.7534 (mttt) cc_final: 0.7321 (mtpp) REVERT: E 160 LYS cc_start: 0.6927 (mttm) cc_final: 0.6716 (mptt) REVERT: E 166 VAL cc_start: 0.8903 (t) cc_final: 0.8547 (p) REVERT: E 213 ILE cc_start: 0.8063 (mt) cc_final: 0.7779 (mt) REVERT: E 258 ASP cc_start: 0.7184 (p0) cc_final: 0.6632 (p0) REVERT: E 259 TYR cc_start: 0.6589 (m-10) cc_final: 0.6002 (m-80) REVERT: E 288 GLN cc_start: 0.7800 (mt0) cc_final: 0.7552 (mt0) REVERT: E 303 LYS cc_start: 0.8945 (mmtm) cc_final: 0.8700 (mmtm) REVERT: E 338 GLU cc_start: 0.7003 (tp30) cc_final: 0.6758 (tp30) REVERT: E 342 GLU cc_start: 0.7586 (tp30) cc_final: 0.7236 (tp30) REVERT: E 414 LYS cc_start: 0.7190 (mmmt) cc_final: 0.6895 (mmtm) REVERT: E 583 MET cc_start: 0.8716 (mtp) cc_final: 0.8454 (mtp) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.1506 time to fit residues: 47.5432 Evaluate side-chains 202 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.188098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.159144 restraints weight = 23772.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.163814 restraints weight = 14428.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.167089 restraints weight = 9799.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.169391 restraints weight = 7243.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.171085 restraints weight = 5708.790| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4381 r_free = 0.4381 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 (11 function evaluations) r_final: 0.4381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.3669 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= 0.154 Angle : 0.661 9.581 16547 Z= 0.355 Chirality : 0.047 0.302 1896 Planarity : 0.004 0.055 1892 Dihedral : 19.568 163.021 2087 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.24 % Favored : 89.54 % Rotamer: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 (0.22), residues: 1319 helix: -1.42 (0.28), residues: 308 sheet: -1.16 (0.29), residues: 322 loop : -2.72 (0.21), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 227 TYR 0.020 0.002 TYR C 200 PHE 0.031 0.002 PHE C 109 TRP 0.014 0.002 TRP E 431 HIS 0.002 0.001 HIS E 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (12074) covalent geometry : angle 0.66112 / 0.36 (16547) hydrogen bonds : bond 0.04481 / 2.82 ( 386) hydrogen bonds : angle 6.58169 / 4.52 ( 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 : 0.427 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: A 12 PHE cc_start: 0.7520 (t80) cc_final: 0.7306 (t80) REVERT: A 24 ASP cc_start: 0.7033 (t0) cc_final: 0.6311 (t0) REVERT: A 29 ASN cc_start: 0.6226 (m110) cc_final: 0.5216 (m110) REVERT: A 78 ILE cc_start: 0.8673 (mm) cc_final: 0.8204 (tp) REVERT: A 114 TYR cc_start: 0.6590 (m-10) cc_final: 0.6325 (m-10) REVERT: B 16 ARG cc_start: 0.7952 (ttm170) cc_final: 0.7689 (ttm-80) REVERT: B 59 PHE cc_start: 0.7490 (t80) cc_final: 0.7234 (t80) REVERT: B 68 ILE cc_start: 0.8048 (mp) cc_final: 0.7662 (mp) REVERT: B 145 GLU cc_start: 0.6948 (mm-30) cc_final: 0.6708 (mm-30) REVERT: B 156 HIS cc_start: 0.6815 (p90) cc_final: 0.6353 (p-80) REVERT: B 196 TYR cc_start: 0.7031 (m-80) cc_final: 0.6305 (m-10) REVERT: B 199 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7234 (tm-30) REVERT: B 218 PHE cc_start: 0.8228 (t80) cc_final: 0.6611 (t80) REVERT: B 227 ARG cc_start: 0.6185 (tpp80) cc_final: 0.5898 (mmm160) REVERT: C 78 LEU cc_start: 0.7837 (mt) cc_final: 0.7630 (mt) REVERT: C 84 LYS cc_start: 0.8613 (tptp) cc_final: 0.8359 (tptp) REVERT: C 85 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6876 (mp0) REVERT: C 112 ARG cc_start: 0.7438 (ptm-80) cc_final: 0.6812 (ptm-80) REVERT: C 156 GLU cc_start: 0.6613 (mp0) cc_final: 0.6235 (mp0) REVERT: C 187 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6168 (tm-30) REVERT: E 53 PHE cc_start: 0.6837 (p90) cc_final: 0.6429 (p90) REVERT: E 54 LEU cc_start: 0.8502 (mm) cc_final: 0.8062 (mt) REVERT: E 66 LEU cc_start: 0.7691 (mt) cc_final: 0.7450 (mm) REVERT: E 99 LYS cc_start: 0.8204 (tttt) cc_final: 0.7909 (tttt) REVERT: E 213 ILE cc_start: 0.8067 (mt) cc_final: 0.7772 (mt) REVERT: E 258 ASP cc_start: 0.7202 (p0) cc_final: 0.6636 (p0) REVERT: E 259 TYR cc_start: 0.6525 (m-10) cc_final: 0.5789 (m-80) REVERT: E 288 GLN cc_start: 0.7754 (mt0) cc_final: 0.7521 (mt0) REVERT: E 303 LYS cc_start: 0.8948 (mmtm) cc_final: 0.8684 (mmtm) REVERT: E 304 GLU cc_start: 0.7419 (pm20) cc_final: 0.7161 (pm20) REVERT: E 338 GLU cc_start: 0.7037 (tp30) cc_final: 0.6781 (tp30) REVERT: E 342 GLU cc_start: 0.7609 (tp30) cc_final: 0.7316 (tp30) REVERT: E 343 TYR cc_start: 0.6901 (m-80) cc_final: 0.6475 (m-10) REVERT: E 414 LYS cc_start: 0.7253 (mmmt) cc_final: 0.6848 (mmtm) REVERT: E 583 MET cc_start: 0.8722 (mtp) cc_final: 0.8452 (mtp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1517 time to fit residues: 46.4350 Evaluate side-chains 196 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 129 optimal weight: 0.9980 chunk 84 optimal weight: 0.0030 chunk 131 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 21 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.189533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.160491 restraints weight = 23826.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.165132 restraints weight = 14496.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.168394 restraints weight = 9853.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.170744 restraints weight = 7289.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.172235 restraints weight = 5744.682| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4395 r_free = 0.4395 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4395 r_free = 0.4395 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.4395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12074 Z= 0.140 Angle : 0.654 8.483 16547 Z= 0.352 Chirality : 0.048 0.281 1896 Planarity : 0.004 0.055 1892 Dihedral : 19.584 162.989 2087 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.31 % Favored : 89.46 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % 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: -2.93 (0.22), residues: 1319 helix: -1.29 (0.29), residues: 301 sheet: -1.10 (0.30), residues: 300 loop : -2.70 (0.21), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG B 227 TYR 0.018 0.002 TYR C 73 PHE 0.032 0.002 PHE C 128 TRP 0.017 0.002 TRP E 431 HIS 0.002 0.001 HIS E 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (12074) covalent geometry : angle 0.65371 / 0.35 (16547) hydrogen bonds : bond 0.04217 / 2.68 ( 386) hydrogen bonds : angle 6.48116 / 4.47 ( 988) *********************** REFINEMENT MACRO_CYCLE 6 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 228 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.436 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 12 PHE cc_start: 0.7512 (t80) cc_final: 0.7311 (t80) REVERT: A 24 ASP cc_start: 0.7146 (t0) cc_final: 0.6488 (t0) REVERT: A 29 ASN cc_start: 0.6150 (m110) cc_final: 0.5129 (m110) REVERT: A 78 ILE cc_start: 0.8657 (mm) cc_final: 0.8183 (tp) REVERT: A 164 ASP cc_start: 0.7898 (t0) cc_final: 0.5929 (t0) REVERT: A 183 LYS cc_start: 0.9024 (tttt) cc_final: 0.8766 (mmtm) REVERT: B 16 ARG cc_start: 0.7939 (ttm170) cc_final: 0.7663 (ttm-80) REVERT: B 145 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6513 (mm-30) REVERT: B 156 HIS cc_start: 0.6736 (p90) cc_final: 0.6285 (p-80) REVERT: B 158 LYS cc_start: 0.8077 (tptp) cc_final: 0.7853 (tppt) REVERT: B 199 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7209 (tm-30) REVERT: C 78 LEU cc_start: 0.7815 (mt) cc_final: 0.7547 (mt) REVERT: C 79 LYS cc_start: 0.7751 (pttt) cc_final: 0.7501 (pttm) REVERT: C 84 LYS cc_start: 0.8628 (tptp) cc_final: 0.8347 (tptp) REVERT: C 85 GLU cc_start: 0.7501 (mt-10) cc_final: 0.6862 (mp0) REVERT: C 112 ARG cc_start: 0.7264 (ptm-80) cc_final: 0.6744 (ptm-80) REVERT: C 156 GLU cc_start: 0.6633 (mp0) cc_final: 0.6258 (mp0) REVERT: C 187 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6194 (tm-30) REVERT: E 54 LEU cc_start: 0.8479 (mm) cc_final: 0.8068 (mt) REVERT: E 66 LEU cc_start: 0.7736 (mt) cc_final: 0.7423 (mt) REVERT: E 99 LYS cc_start: 0.8233 (tttt) cc_final: 0.7898 (tttt) REVERT: E 258 ASP cc_start: 0.7186 (p0) cc_final: 0.6595 (p0) REVERT: E 288 GLN cc_start: 0.7714 (mt0) cc_final: 0.7473 (mt0) REVERT: E 303 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8678 (mmtm) REVERT: E 304 GLU cc_start: 0.7431 (pm20) cc_final: 0.7012 (pm20) REVERT: E 338 GLU cc_start: 0.6937 (tp30) cc_final: 0.6680 (tp30) REVERT: E 342 GLU cc_start: 0.7620 (tp30) cc_final: 0.7332 (tp30) REVERT: E 343 TYR cc_start: 0.7047 (m-80) cc_final: 0.6647 (m-10) REVERT: E 414 LYS cc_start: 0.7285 (mmmt) cc_final: 0.6852 (mmtm) REVERT: E 583 MET cc_start: 0.8718 (mtp) cc_final: 0.8479 (mtp) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1529 time to fit residues: 46.3800 Evaluate side-chains 199 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 111 optimal weight: 0.0070 chunk 3 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 16 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.4606 r_free = 0.4606 target = 0.190434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.162070 restraints weight = 23969.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.166625 restraints weight = 14619.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.169847 restraints weight = 10001.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.172105 restraints weight = 7432.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.173807 restraints weight = 5893.361| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4412 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4412 r_free = 0.4412 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4412 r_free = 0.4412 target_work(ls_wunit_k1) = 0.174 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12074 Z= 0.134 Angle : 0.665 9.161 16547 Z= 0.353 Chirality : 0.047 0.277 1896 Planarity : 0.004 0.055 1892 Dihedral : 19.569 163.641 2087 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.70 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: -2.89 (0.22), residues: 1319 helix: -1.30 (0.29), residues: 301 sheet: -1.06 (0.30), residues: 302 loop : -2.66 (0.21), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 209 TYR 0.018 0.002 TYR B 13 PHE 0.032 0.002 PHE C 109 TRP 0.018 0.002 TRP E 429 HIS 0.002 0.000 HIS E 510 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (12074) covalent geometry : angle 0.66497 / 0.35 (16547) hydrogen bonds : bond 0.04084 / 2.56 ( 386) hydrogen bonds : angle 6.33670 / 4.36 ( 988) *********************** REFINEMENT MACRO_CYCLE 7 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 225 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.429 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 12 PHE cc_start: 0.7455 (t80) cc_final: 0.7250 (t80) REVERT: A 24 ASP cc_start: 0.7139 (t0) cc_final: 0.6520 (t0) REVERT: A 26 ILE cc_start: 0.7719 (pt) cc_final: 0.7445 (pt) REVERT: A 29 ASN cc_start: 0.6066 (m110) cc_final: 0.4994 (m110) REVERT: A 78 ILE cc_start: 0.8661 (mm) cc_final: 0.8212 (tp) REVERT: A 164 ASP cc_start: 0.7872 (t0) cc_final: 0.5949 (t0) REVERT: A 183 LYS cc_start: 0.9011 (tttt) cc_final: 0.8580 (tppt) REVERT: A 244 TRP cc_start: 0.6492 (m100) cc_final: 0.6024 (m100) REVERT: B 59 PHE cc_start: 0.7604 (t80) cc_final: 0.7326 (t80) REVERT: B 68 ILE cc_start: 0.7852 (mp) cc_final: 0.7590 (mp) REVERT: B 145 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6582 (mm-30) REVERT: B 156 HIS cc_start: 0.6740 (p90) cc_final: 0.6295 (p-80) REVERT: B 158 LYS cc_start: 0.8055 (tptp) cc_final: 0.7772 (tppt) REVERT: B 199 GLU cc_start: 0.7371 (tm-30) cc_final: 0.7159 (tm-30) REVERT: B 218 PHE cc_start: 0.8243 (t80) cc_final: 0.6422 (t80) REVERT: B 227 ARG cc_start: 0.5471 (tpp80) cc_final: 0.5082 (tpt-90) REVERT: C 78 LEU cc_start: 0.7883 (mt) cc_final: 0.7583 (mt) REVERT: C 84 LYS cc_start: 0.8513 (tptp) cc_final: 0.8298 (tptp) REVERT: C 85 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6811 (mp0) REVERT: C 112 ARG cc_start: 0.7280 (ptm-80) cc_final: 0.6778 (ptm-80) REVERT: C 187 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6134 (tm-30) REVERT: E 54 LEU cc_start: 0.8516 (mm) cc_final: 0.8271 (mt) REVERT: E 66 LEU cc_start: 0.7675 (mt) cc_final: 0.7376 (mt) REVERT: E 99 LYS cc_start: 0.8144 (tttt) cc_final: 0.7821 (tttt) REVERT: E 123 GLU cc_start: 0.6656 (tm-30) cc_final: 0.6221 (tm-30) REVERT: E 233 ILE cc_start: 0.6930 (mp) cc_final: 0.6484 (tt) REVERT: E 288 GLN cc_start: 0.7663 (mt0) cc_final: 0.7416 (mt0) REVERT: E 303 LYS cc_start: 0.8919 (mmtm) cc_final: 0.8687 (mmtm) REVERT: E 304 GLU cc_start: 0.7343 (pm20) cc_final: 0.6948 (pm20) REVERT: E 338 GLU cc_start: 0.6804 (tp30) cc_final: 0.6291 (tp30) REVERT: E 342 GLU cc_start: 0.7555 (tp30) cc_final: 0.7186 (tp30) REVERT: E 343 TYR cc_start: 0.7028 (m-80) cc_final: 0.6718 (m-10) REVERT: E 583 MET cc_start: 0.8720 (mtp) cc_final: 0.8470 (mtp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1585 time to fit residues: 47.1782 Evaluate side-chains 194 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4595 r_free = 0.4595 target = 0.189482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.160584 restraints weight = 24075.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.165185 restraints weight = 14619.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.168487 restraints weight = 9945.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.170816 restraints weight = 7394.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.172468 restraints weight = 5841.422| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4399 r_free = 0.4399 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4399 r_free = 0.4399 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.4399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6046 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12074 Z= 0.144 Angle : 0.666 9.114 16547 Z= 0.353 Chirality : 0.047 0.270 1896 Planarity : 0.004 0.055 1892 Dihedral : 19.572 164.067 2087 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.61 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % 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: -2.81 (0.22), residues: 1319 helix: -1.19 (0.29), residues: 300 sheet: -1.03 (0.30), residues: 309 loop : -2.64 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 248 TYR 0.017 0.002 TYR C 73 PHE 0.025 0.002 PHE C 128 TRP 0.015 0.002 TRP E 429 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (12074) covalent geometry : angle 0.66596 / 0.35 (16547) hydrogen bonds : bond 0.04093 / 2.59 ( 386) hydrogen bonds : angle 6.23296 / 4.29 ( 988) *********************** REFINEMENT MACRO_CYCLE 8 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 219 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.478 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: A 24 ASP cc_start: 0.7014 (t0) cc_final: 0.6408 (t0) REVERT: A 29 ASN cc_start: 0.5813 (m110) cc_final: 0.4496 (m110) REVERT: A 76 LYS cc_start: 0.7557 (tptt) cc_final: 0.7344 (tptt) REVERT: A 78 ILE cc_start: 0.8698 (mm) cc_final: 0.8238 (tp) REVERT: A 116 LYS cc_start: 0.8318 (tptp) cc_final: 0.7973 (ttmm) REVERT: A 164 ASP cc_start: 0.7888 (t0) cc_final: 0.5989 (t0) REVERT: A 183 LYS cc_start: 0.8992 (tttt) cc_final: 0.8559 (tppt) REVERT: A 244 TRP cc_start: 0.6537 (m100) cc_final: 0.6059 (m100) REVERT: B 59 PHE cc_start: 0.7632 (t80) cc_final: 0.7368 (t80) REVERT: B 68 ILE cc_start: 0.7900 (mp) cc_final: 0.7633 (mp) REVERT: B 145 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6653 (mm-30) REVERT: B 156 HIS cc_start: 0.6741 (p90) cc_final: 0.6241 (p-80) REVERT: B 158 LYS cc_start: 0.8080 (tptp) cc_final: 0.7865 (tppt) REVERT: B 199 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7217 (tm-30) REVERT: B 218 PHE cc_start: 0.8228 (t80) cc_final: 0.6210 (t80) REVERT: C 78 LEU cc_start: 0.7825 (mt) cc_final: 0.7551 (mt) REVERT: C 79 LYS cc_start: 0.7721 (pttt) cc_final: 0.7436 (pttm) REVERT: C 84 LYS cc_start: 0.8592 (tptp) cc_final: 0.8308 (tptp) REVERT: C 85 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6885 (mp0) REVERT: C 95 ASP cc_start: 0.8592 (m-30) cc_final: 0.8372 (m-30) REVERT: C 112 ARG cc_start: 0.7215 (ptm-80) cc_final: 0.6781 (ptm-80) REVERT: C 187 GLU cc_start: 0.6979 (tm-30) cc_final: 0.6153 (tm-30) REVERT: E 66 LEU cc_start: 0.7734 (mt) cc_final: 0.7368 (mt) REVERT: E 99 LYS cc_start: 0.8211 (tttt) cc_final: 0.7912 (tttt) REVERT: E 183 MET cc_start: 0.7239 (tpp) cc_final: 0.6861 (tpp) REVERT: E 209 ASN cc_start: 0.6237 (m-40) cc_final: 0.6027 (m-40) REVERT: E 228 GLN cc_start: 0.5653 (pm20) cc_final: 0.5346 (pm20) REVERT: E 233 ILE cc_start: 0.6990 (mp) cc_final: 0.6539 (tt) REVERT: E 288 GLN cc_start: 0.7728 (mt0) cc_final: 0.7477 (mt0) REVERT: E 303 LYS cc_start: 0.8918 (mmtm) cc_final: 0.8682 (mmtm) REVERT: E 304 GLU cc_start: 0.7458 (pm20) cc_final: 0.7031 (pm20) REVERT: E 338 GLU cc_start: 0.6977 (tp30) cc_final: 0.6406 (tp30) REVERT: E 342 GLU cc_start: 0.7628 (tp30) cc_final: 0.7250 (tp30) REVERT: E 343 TYR cc_start: 0.7018 (m-80) cc_final: 0.6728 (m-10) REVERT: E 430 LEU cc_start: 0.8117 (tt) cc_final: 0.7910 (tt) REVERT: E 583 MET cc_start: 0.8711 (mtp) cc_final: 0.8478 (mtp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1438 time to fit residues: 42.4132 Evaluate side-chains 194 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4548 r_free = 0.4548 target = 0.185729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.155629 restraints weight = 23683.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.160165 restraints weight = 14570.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.163362 restraints weight = 9989.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.165601 restraints weight = 7454.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.167300 restraints weight = 5954.529| |-----------------------------------------------------------------------------| r_work (final): 0.4310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4317 r_free = 0.4317 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4317 r_free = 0.4317 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.4317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 12074 Z= 0.278 Angle : 0.813 9.630 16547 Z= 0.434 Chirality : 0.051 0.317 1896 Planarity : 0.005 0.053 1892 Dihedral : 19.663 164.513 2087 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.89 % Favored : 86.88 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -3.12 (0.21), residues: 1319 helix: -1.59 (0.27), residues: 306 sheet: -1.26 (0.29), residues: 323 loop : -2.76 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 248 TYR 0.030 0.003 TYR B 55 PHE 0.027 0.003 PHE C 128 TRP 0.028 0.003 TRP E 429 HIS 0.006 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.28 (12074) covalent geometry : angle 0.81306 / 0.43 (16547) hydrogen bonds : bond 0.06036 / 3.74 ( 386) hydrogen bonds : angle 6.68881 / 4.65 ( 988) *********************** REFINEMENT MACRO_CYCLE 9 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 225 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.432 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: A 24 ASP cc_start: 0.7199 (t0) cc_final: 0.6563 (t0) REVERT: A 76 LYS cc_start: 0.7814 (tptt) cc_final: 0.7596 (tptt) REVERT: A 78 ILE cc_start: 0.8727 (mm) cc_final: 0.8366 (tp) REVERT: A 107 SER cc_start: 0.7800 (p) cc_final: 0.7564 (m) REVERT: A 116 LYS cc_start: 0.8376 (tptp) cc_final: 0.8001 (mtpp) REVERT: A 164 ASP cc_start: 0.7799 (t0) cc_final: 0.6237 (t0) REVERT: A 183 LYS cc_start: 0.8967 (tttt) cc_final: 0.8559 (tppt) REVERT: A 244 TRP cc_start: 0.6766 (m100) cc_final: 0.6281 (m100) REVERT: B 145 GLU cc_start: 0.7125 (mm-30) cc_final: 0.6805 (mm-30) REVERT: B 156 HIS cc_start: 0.6776 (p90) cc_final: 0.6554 (p-80) REVERT: B 158 LYS cc_start: 0.8143 (tptp) cc_final: 0.7920 (tppt) REVERT: B 199 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7325 (tm-30) REVERT: B 227 ARG cc_start: 0.6248 (tpp80) cc_final: 0.5938 (tpp80) REVERT: C 1 MET cc_start: 0.6853 (tmm) cc_final: 0.6553 (tmm) REVERT: C 78 LEU cc_start: 0.7876 (mt) cc_final: 0.7569 (mt) REVERT: C 79 LYS cc_start: 0.7726 (pttt) cc_final: 0.7522 (pttm) REVERT: C 84 LYS cc_start: 0.8617 (tptp) cc_final: 0.8268 (tptp) REVERT: C 85 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7100 (mp0) REVERT: C 187 GLU cc_start: 0.7453 (tm-30) cc_final: 0.6485 (tm-30) REVERT: E 66 LEU cc_start: 0.7827 (mt) cc_final: 0.7520 (mt) REVERT: E 99 LYS cc_start: 0.8352 (tttt) cc_final: 0.8087 (tttt) REVERT: E 123 GLU cc_start: 0.6392 (tm-30) cc_final: 0.6149 (tm-30) REVERT: E 143 LYS cc_start: 0.7066 (mtpt) cc_final: 0.6865 (ptpp) REVERT: E 183 MET cc_start: 0.7117 (tpp) cc_final: 0.6672 (tpp) REVERT: E 209 ASN cc_start: 0.6432 (m-40) cc_final: 0.6163 (m-40) REVERT: E 259 TYR cc_start: 0.6214 (m-80) cc_final: 0.6005 (m-10) REVERT: E 288 GLN cc_start: 0.7953 (mt0) cc_final: 0.7744 (mt0) REVERT: E 303 LYS cc_start: 0.8846 (mmtm) cc_final: 0.8581 (mmtm) REVERT: E 338 GLU cc_start: 0.7218 (tp30) cc_final: 0.6937 (tp30) REVERT: E 342 GLU cc_start: 0.7802 (tp30) cc_final: 0.7447 (tp30) REVERT: E 414 LYS cc_start: 0.7173 (mmmt) cc_final: 0.6887 (mmmt) REVERT: E 583 MET cc_start: 0.8730 (mtp) cc_final: 0.8485 (mtp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1409 time to fit residues: 42.7106 Evaluate side-chains 193 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 95 optimal weight: 0.0010 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 ASN E 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.189643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.159780 restraints weight = 23993.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.164535 restraints weight = 14667.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.167763 restraints weight = 10003.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 76)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.170183 restraints weight = 7468.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.171856 restraints weight = 5906.221| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4373 r_free = 0.4373 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4373 r_free = 0.4373 target_work(ls_wunit_k1) = 0.170 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12074 Z= 0.155 Angle : 0.716 9.358 16547 Z= 0.379 Chirality : 0.049 0.283 1896 Planarity : 0.004 0.054 1892 Dihedral : 19.714 164.345 2087 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.77 % Favored : 89.08 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -1.42 (0.28), residues: 307 sheet: -1.04 (0.31), residues: 303 loop : -2.64 (0.21), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 35 TYR 0.038 0.002 TYR B 13 PHE 0.025 0.002 PHE B 27 TRP 0.013 0.002 TRP E 50 HIS 0.005 0.001 HIS C 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (12074) covalent geometry : angle 0.71633 / 0.38 (16547) hydrogen bonds : bond 0.04476 / 2.77 ( 386) hydrogen bonds : angle 6.42986 / 4.45 ( 988) ********************** REFINEMENT MACRO_CYCLE 10 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 224 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.416 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: A 3 LYS cc_start: 0.7582 (ptpp) cc_final: 0.7086 (ptpp) REVERT: A 24 ASP cc_start: 0.7118 (t0) cc_final: 0.6516 (t0) REVERT: A 29 ASN cc_start: 0.6918 (t0) cc_final: 0.6702 (m110) REVERT: A 50 MET cc_start: 0.4716 (tmm) cc_final: 0.4491 (tmm) REVERT: A 76 LYS cc_start: 0.7685 (tptt) cc_final: 0.7412 (tptp) REVERT: A 78 ILE cc_start: 0.8628 (mm) cc_final: 0.8257 (tp) REVERT: A 116 LYS cc_start: 0.8375 (tptp) cc_final: 0.8069 (ttmm) REVERT: A 164 ASP cc_start: 0.7773 (t0) cc_final: 0.6491 (t0) REVERT: A 183 LYS cc_start: 0.8959 (tttt) cc_final: 0.8497 (tppt) REVERT: A 244 TRP cc_start: 0.6762 (m100) cc_final: 0.6239 (m100) REVERT: B 1 MET cc_start: 0.4516 (tpp) cc_final: 0.3487 (tpt) REVERT: B 16 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7627 (ttm-80) REVERT: B 59 PHE cc_start: 0.7671 (t80) cc_final: 0.7384 (t80) REVERT: B 145 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6729 (mm-30) REVERT: B 156 HIS cc_start: 0.6780 (p90) cc_final: 0.6283 (p-80) REVERT: B 158 LYS cc_start: 0.8133 (tptp) cc_final: 0.7902 (tppt) REVERT: B 199 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7265 (tm-30) REVERT: C 84 LYS cc_start: 0.8651 (tptp) cc_final: 0.8439 (tptp) REVERT: C 85 GLU cc_start: 0.7544 (mt-10) cc_final: 0.6864 (mp0) REVERT: C 187 GLU cc_start: 0.7374 (tm-30) cc_final: 0.6322 (tm-30) REVERT: E 54 LEU cc_start: 0.8538 (mm) cc_final: 0.8319 (mm) REVERT: E 66 LEU cc_start: 0.7742 (mt) cc_final: 0.7415 (mt) REVERT: E 99 LYS cc_start: 0.8227 (tttt) cc_final: 0.7982 (tttt) REVERT: E 160 LYS cc_start: 0.7467 (ptpt) cc_final: 0.7076 (ptpp) REVERT: E 183 MET cc_start: 0.7055 (tpp) cc_final: 0.6602 (tpp) REVERT: E 228 GLN cc_start: 0.5667 (pm20) cc_final: 0.5307 (pm20) REVERT: E 233 ILE cc_start: 0.7036 (mp) cc_final: 0.6766 (mt) REVERT: E 258 ASP cc_start: 0.6816 (p0) cc_final: 0.6605 (p0) REVERT: E 259 TYR cc_start: 0.6182 (m-80) cc_final: 0.5946 (m-80) REVERT: E 288 GLN cc_start: 0.7832 (mt0) cc_final: 0.7599 (mt0) REVERT: E 303 LYS cc_start: 0.8809 (mmtm) cc_final: 0.8422 (mmtm) REVERT: E 308 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6912 (tm-30) REVERT: E 338 GLU cc_start: 0.7022 (tp30) cc_final: 0.6448 (tp30) REVERT: E 342 GLU cc_start: 0.7750 (tp30) cc_final: 0.7409 (tp30) REVERT: E 343 TYR cc_start: 0.7051 (m-80) cc_final: 0.6716 (m-10) REVERT: E 583 MET cc_start: 0.8715 (mtp) cc_final: 0.8481 (mtp) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1458 time to fit residues: 43.5985 Evaluate side-chains 191 residues out of total 1167 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 134 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 35 optimal weight: 0.3980 chunk 6 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 232 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 = 0.4612 r_free = 0.4612 target = 0.190790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.161464 restraints weight = 23782.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.166197 restraints weight = 14414.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.169510 restraints weight = 9762.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.171814 restraints weight = 7209.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.173590 restraints weight = 5694.903| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4395 r_free = 0.4395 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4395 r_free = 0.4395 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.4395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12074 Z= 0.141 Angle : 0.695 8.865 16547 Z= 0.369 Chirality : 0.048 0.278 1896 Planarity : 0.004 0.055 1892 Dihedral : 19.720 165.104 2087 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.61 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -2.89 (0.22), residues: 1319 helix: -1.43 (0.28), residues: 314 sheet: -1.04 (0.30), residues: 302 loop : -2.61 (0.21), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 35 TYR 0.036 0.002 TYR B 13 PHE 0.028 0.002 PHE B 27 TRP 0.016 0.002 TRP E 431 HIS 0.002 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (12074) covalent geometry : angle 0.69520 / 0.37 (16547) hydrogen bonds : bond 0.04076 / 2.55 ( 386) hydrogen bonds : angle 6.22692 / 4.32 ( 988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.64 seconds wall clock time: 43 minutes 51.55 seconds (2631.55 seconds total)