Starting phenix.real_space_refine on Fri Mar 15 13:27:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/03_2024/7rpx_24625.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/03_2024/7rpx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/03_2024/7rpx_24625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/03_2024/7rpx_24625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/03_2024/7rpx_24625.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/03_2024/7rpx_24625.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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 Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 6.51, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 3.84 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: 4.13 Time building geometry restraints manager: 4.93 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=" N MET A 182 " pdb=" CA MET A 182 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.31e-02 5.83e+03 6.89e+00 bond pdb=" N LYS A 183 " pdb=" CA LYS A 183 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.35e+00 bond pdb=" N ASP A 184 " pdb=" CA ASP A 184 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.99e+00 bond pdb=" N LEU A 187 " pdb=" CA LEU A 187 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.41e+00 bond pdb=" N LYS A 185 " pdb=" CA LYS A 185 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.41e-02 5.03e+03 4.72e+00 ... (remaining 12069 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.55: 610 106.55 - 113.43: 6680 113.43 - 120.30: 4346 120.30 - 127.17: 4731 127.17 - 134.05: 180 Bond angle restraints: 16547 Sorted by residual: 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 angle pdb=" OP1 DG X 25 " pdb=" P DG X 25 " pdb=" OP2 DG X 25 " ideal model delta sigma weight residual 120.00 109.39 10.61 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O MET A 182 " pdb=" C MET A 182 " pdb=" N LYS A 183 " ideal model delta sigma weight residual 122.96 126.60 -3.64 1.13e+00 7.83e-01 1.04e+01 angle pdb=" N GLY E 173 " pdb=" CA GLY E 173 " pdb=" C GLY E 173 " ideal model delta sigma weight residual 115.63 111.19 4.44 1.49e+00 4.50e-01 8.89e+00 angle pdb=" N ASP A 55 " pdb=" CA ASP A 55 " pdb=" C ASP A 55 " ideal model delta sigma weight residual 114.56 110.82 3.74 1.27e+00 6.20e-01 8.69e+00 ... (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 - 0.079: 1749 0.079 - 0.157: 145 0.157 - 0.236: 1 0.236 - 0.315: 0 0.315 - 0.393: 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 2.35 -2.74 -0.39 2.00e-01 2.50e+01 3.87e+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=" CA ILE E 233 " pdb=" N ILE E 233 " pdb=" C ILE E 233 " pdb=" CB ILE E 233 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-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 ========== 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: 0.310 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: 2.010 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 35.880 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6087 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12074 Z= 0.187 Angle : 0.556 10.609 16547 Z= 0.311 Chirality : 0.042 0.393 1896 Planarity : 0.003 0.051 1892 Dihedral : 15.951 161.418 4710 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 21.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.001 TRP E 431 HIS 0.002 0.001 HIS B 156 PHE 0.014 0.001 PHE B 101 TYR 0.022 0.001 TYR C 200 ARG 0.002 0.000 ARG E 140 *********************** 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 fitting. rotamer outliers: 10 poor density : 294 time to evaluate : 1.219 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: 0.7117 (t80) REVERT: A 24 ASP cc_start: 0.6700 (t0) cc_final: 0.6020 (t0) REVERT: A 26 ILE cc_start: 0.8107 (pt) cc_final: 0.7893 (pt) REVERT: A 29 ASN cc_start: 0.6231 (m-40) cc_final: 0.5651 (m110) REVERT: A 30 PHE cc_start: 0.8159 (m-80) cc_final: 0.7950 (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: 0.7307 (pptt) REVERT: A 164 ASP cc_start: 0.7677 (t0) cc_final: 0.5804 (t0) REVERT: A 182 MET cc_start: 0.4462 (mmm) cc_final: 0.4132 (mmm) REVERT: A 183 LYS cc_start: 0.8935 (tttt) cc_final: 0.8655 (mmtm) REVERT: A 210 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8307 (ptpt) REVERT: A 213 ARG cc_start: 0.5305 (OUTLIER) cc_final: 0.4583 (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: 0.6347 (t80) REVERT: B 16 ARG cc_start: 0.7724 (mtm180) cc_final: 0.7434 (ttm-80) REVERT: B 55 TYR cc_start: 0.4681 (OUTLIER) cc_final: 0.1756 (t80) REVERT: B 68 ILE cc_start: 0.8603 (mt) cc_final: 0.8101 (mm) REVERT: B 156 HIS cc_start: 0.6875 (p90) cc_final: 0.6503 (p-80) REVERT: B 191 ASP cc_start: 0.7241 (m-30) cc_final: 0.6496 (m-30) REVERT: C 70 ASN cc_start: 0.4626 (t0) cc_final: 0.4310 (t0) REVERT: C 83 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7831 (mpp80) REVERT: C 128 PHE cc_start: 0.6684 (m-80) cc_final: 0.4537 (m-10) REVERT: C 165 LYS cc_start: 0.6958 (pttp) cc_final: 0.6606 (pttp) REVERT: E 145 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.4526 (ttm-80) REVERT: E 162 LEU cc_start: 0.7773 (mt) cc_final: 0.7253 (mt) REVERT: E 213 ILE cc_start: 0.8145 (mt) cc_final: 0.7721 (mt) REVERT: E 303 LYS cc_start: 0.8829 (mptp) cc_final: 0.8517 (mmtm) REVERT: E 454 PHE cc_start: 0.5176 (m-80) cc_final: 0.3298 (m-80) REVERT: E 517 MET cc_start: 0.5501 (ttm) cc_final: 0.5172 (ttm) REVERT: E 583 MET cc_start: 0.8854 (mtp) cc_final: 0.8508 (mtp) outliers start: 10 outliers final: 2 residues processed: 302 average time/residue: 0.3275 time to fit residues: 128.3706 Evaluate side-chains 221 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 0.0970 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 0.2980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 GLN E 288 GLN E 386 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6039 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12074 Z= 0.209 Angle : 0.663 9.609 16547 Z= 0.353 Chirality : 0.047 0.224 1896 Planarity : 0.005 0.054 1892 Dihedral : 19.286 159.740 2087 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.48 % Favored : 90.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.22), residues: 1319 helix: -1.09 (0.29), residues: 307 sheet: -0.79 (0.29), residues: 334 loop : -2.58 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 431 HIS 0.002 0.001 HIS C 43 PHE 0.028 0.002 PHE E 400 TYR 0.016 0.002 TYR B 13 ARG 0.005 0.000 ARG B 227 *********************** 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 fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 1.333 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: 0.6823 (t0) cc_final: 0.6101 (t0) REVERT: A 164 ASP cc_start: 0.7689 (t0) cc_final: 0.6275 (t0) REVERT: A 165 LYS cc_start: 0.8427 (pttm) cc_final: 0.7906 (pttm) REVERT: A 182 MET cc_start: 0.3871 (mmm) cc_final: 0.3626 (mmm) REVERT: A 183 LYS cc_start: 0.9092 (tttt) cc_final: 0.8872 (mmtm) REVERT: A 184 ASP cc_start: 0.7579 (t0) cc_final: 0.7105 (t0) REVERT: A 185 LYS cc_start: 0.8156 (mmtm) cc_final: 0.7871 (mmmm) REVERT: A 210 LYS cc_start: 0.8733 (ptmt) cc_final: 0.8044 (ptpp) REVERT: A 244 TRP cc_start: 0.6914 (m100) cc_final: 0.6686 (m100) REVERT: B 16 ARG cc_start: 0.7634 (mtm180) cc_final: 0.7424 (ttm-80) REVERT: B 68 ILE cc_start: 0.8232 (mt) cc_final: 0.7932 (mp) REVERT: B 145 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6728 (mm-30) REVERT: B 156 HIS cc_start: 0.6982 (p90) cc_final: 0.6534 (p-80) REVERT: C 78 LEU cc_start: 0.7883 (mt) cc_final: 0.7681 (mt) REVERT: C 79 LYS cc_start: 0.7868 (pttt) cc_final: 0.7547 (pttt) REVERT: E 123 GLU cc_start: 0.6375 (tm-30) cc_final: 0.5895 (tm-30) REVERT: E 304 GLU cc_start: 0.7415 (pm20) cc_final: 0.7211 (pm20) REVERT: E 338 GLU cc_start: 0.6687 (tp30) cc_final: 0.6224 (tp30) REVERT: E 342 GLU cc_start: 0.7005 (tp30) cc_final: 0.6764 (tp30) REVERT: E 583 MET cc_start: 0.8690 (mtp) cc_final: 0.8464 (mtp) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.3171 time to fit residues: 99.6893 Evaluate side-chains 195 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 42 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12074 Z= 0.258 Angle : 0.677 11.942 16547 Z= 0.360 Chirality : 0.047 0.287 1896 Planarity : 0.004 0.052 1892 Dihedral : 19.256 160.630 2087 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.68 % Favored : 88.10 % Rotamer: Outliers : 0.09 % Allowed : 4.20 % Favored : 95.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.22), residues: 1319 helix: -1.13 (0.29), residues: 301 sheet: -0.92 (0.29), residues: 327 loop : -2.68 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 429 HIS 0.002 0.001 HIS B 156 PHE 0.027 0.002 PHE B 27 TYR 0.023 0.002 TYR C 200 ARG 0.007 0.001 ARG B 35 *********************** 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 230 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7067 (t0) cc_final: 0.6329 (t0) REVERT: A 29 ASN cc_start: 0.6226 (m110) cc_final: 0.5201 (m110) REVERT: A 47 MET cc_start: 0.4294 (ptt) cc_final: 0.3953 (ptt) REVERT: A 163 GLU cc_start: 0.8096 (tp30) cc_final: 0.7884 (mm-30) REVERT: A 165 LYS cc_start: 0.8472 (pttm) cc_final: 0.8024 (pttm) REVERT: A 182 MET cc_start: 0.3808 (mmm) cc_final: 0.3526 (mmm) REVERT: A 244 TRP cc_start: 0.7004 (m100) cc_final: 0.6680 (m100) REVERT: B 68 ILE cc_start: 0.8606 (mt) cc_final: 0.8337 (mp) REVERT: B 156 HIS cc_start: 0.6884 (p90) cc_final: 0.6451 (p-80) REVERT: B 191 ASP cc_start: 0.7676 (m-30) cc_final: 0.7428 (m-30) REVERT: B 199 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7231 (tm-30) REVERT: B 218 PHE cc_start: 0.8417 (t80) cc_final: 0.7591 (t80) REVERT: C 78 LEU cc_start: 0.7995 (mt) cc_final: 0.7778 (mt) REVERT: C 112 ARG cc_start: 0.7335 (ptm-80) cc_final: 0.6818 (ptm-80) REVERT: C 187 GLU cc_start: 0.6144 (tm-30) cc_final: 0.5820 (tm-30) REVERT: E 123 GLU cc_start: 0.6566 (tm-30) cc_final: 0.6170 (tm-30) REVERT: E 258 ASP cc_start: 0.6136 (p0) cc_final: 0.5781 (p0) REVERT: E 304 GLU cc_start: 0.7542 (pm20) cc_final: 0.7235 (pm20) REVERT: E 338 GLU cc_start: 0.6670 (tp30) cc_final: 0.6461 (tp30) REVERT: E 342 GLU cc_start: 0.7235 (tp30) cc_final: 0.6955 (tp30) REVERT: E 583 MET cc_start: 0.8668 (mtp) cc_final: 0.8455 (mtp) outliers start: 1 outliers final: 0 residues processed: 230 average time/residue: 0.3166 time to fit residues: 95.6922 Evaluate side-chains 193 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 0.0050 chunk 59 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 0.9980 chunk 133 optimal weight: 30.0000 chunk 119 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN E 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12074 Z= 0.194 Angle : 0.640 10.067 16547 Z= 0.336 Chirality : 0.045 0.326 1896 Planarity : 0.004 0.054 1892 Dihedral : 19.311 162.523 2087 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.08 % Favored : 89.69 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.22), residues: 1319 helix: -0.87 (0.30), residues: 299 sheet: -0.90 (0.30), residues: 323 loop : -2.61 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 244 HIS 0.001 0.000 HIS B 156 PHE 0.029 0.002 PHE C 128 TYR 0.019 0.002 TYR C 200 ARG 0.006 0.000 ARG B 227 *********************** 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 231 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.020 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: 0.7217 (t0) cc_final: 0.6478 (t0) REVERT: A 29 ASN cc_start: 0.6035 (m110) cc_final: 0.4900 (m110) REVERT: A 91 LEU cc_start: 0.8106 (tp) cc_final: 0.7420 (pt) REVERT: A 164 ASP cc_start: 0.7753 (t0) cc_final: 0.5767 (t0) REVERT: A 165 LYS cc_start: 0.8689 (pttm) cc_final: 0.8464 (pttm) REVERT: A 182 MET cc_start: 0.4193 (mmm) cc_final: 0.3753 (mmm) REVERT: A 244 TRP cc_start: 0.6790 (m100) cc_final: 0.6384 (m100) REVERT: B 68 ILE cc_start: 0.8386 (mt) cc_final: 0.8149 (mp) REVERT: B 145 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6719 (mm-30) REVERT: B 156 HIS cc_start: 0.6831 (p90) cc_final: 0.6340 (p-80) REVERT: B 158 LYS cc_start: 0.8077 (tptp) cc_final: 0.7852 (tppt) REVERT: B 214 MET cc_start: 0.7316 (ttt) cc_final: 0.7069 (ttt) REVERT: B 218 PHE cc_start: 0.8376 (t80) cc_final: 0.7003 (t80) REVERT: C 78 LEU cc_start: 0.7920 (mt) cc_final: 0.7680 (mt) REVERT: E 99 LYS cc_start: 0.7804 (tttt) cc_final: 0.7539 (tttt) REVERT: E 123 GLU cc_start: 0.6758 (tm-30) cc_final: 0.5929 (tm-30) REVERT: E 304 GLU cc_start: 0.7516 (pm20) cc_final: 0.7279 (pm20) REVERT: E 338 GLU cc_start: 0.6488 (tp30) cc_final: 0.6021 (tp30) REVERT: E 342 GLU cc_start: 0.7235 (tp30) cc_final: 0.6856 (tp30) REVERT: E 454 PHE cc_start: 0.5848 (m-80) cc_final: 0.5527 (m-80) REVERT: E 583 MET cc_start: 0.8675 (mtp) cc_final: 0.8465 (mtp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.3307 time to fit residues: 100.5959 Evaluate side-chains 194 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 119 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 ASN E 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.4135 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= 0.396 Angle : 0.799 12.792 16547 Z= 0.420 Chirality : 0.050 0.365 1896 Planarity : 0.005 0.051 1892 Dihedral : 19.471 162.465 2087 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 28.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 13.57 % Favored : 86.20 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.22), residues: 1319 helix: -1.64 (0.27), residues: 304 sheet: -1.00 (0.30), residues: 305 loop : -2.81 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 429 HIS 0.006 0.001 HIS B 156 PHE 0.031 0.003 PHE E 165 TYR 0.029 0.003 TYR A 6 ARG 0.007 0.001 ARG B 227 *********************** 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 234 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.198 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: 0.7163 (t0) cc_final: 0.6507 (t0) REVERT: A 76 LYS cc_start: 0.7606 (tptp) cc_final: 0.7400 (mmmt) REVERT: A 116 LYS cc_start: 0.8339 (tptp) cc_final: 0.8078 (mtpp) REVERT: A 182 MET cc_start: 0.4604 (mmm) cc_final: 0.4212 (mmm) REVERT: B 1 MET cc_start: 0.5934 (tpp) cc_final: 0.5317 (ttm) REVERT: B 68 ILE cc_start: 0.8936 (mt) cc_final: 0.8484 (mm) REVERT: B 145 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6778 (mm-30) REVERT: B 156 HIS cc_start: 0.6861 (p90) cc_final: 0.6614 (p-80) REVERT: C 37 VAL cc_start: 0.7210 (p) cc_final: 0.6974 (t) REVERT: C 78 LEU cc_start: 0.8019 (mt) cc_final: 0.7806 (mt) REVERT: C 79 LYS cc_start: 0.7854 (pttt) cc_final: 0.7633 (pttm) REVERT: C 112 ARG cc_start: 0.7411 (ptm-80) cc_final: 0.6935 (ptm-80) REVERT: C 230 MET cc_start: 0.1749 (mtt) cc_final: 0.1483 (mtp) REVERT: E 66 LEU cc_start: 0.7613 (mt) cc_final: 0.7345 (mt) REVERT: E 123 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6691 (tm-30) REVERT: E 180 LEU cc_start: 0.7712 (mt) cc_final: 0.7440 (mt) REVERT: E 213 ILE cc_start: 0.8070 (mt) cc_final: 0.7468 (mt) REVERT: E 236 MET cc_start: 0.3867 (ppp) cc_final: 0.3066 (ptt) REVERT: E 258 ASP cc_start: 0.6340 (p0) cc_final: 0.6076 (p0) REVERT: E 288 GLN cc_start: 0.7775 (mt0) cc_final: 0.7503 (mt0) REVERT: E 338 GLU cc_start: 0.6907 (tp30) cc_final: 0.6373 (tp30) REVERT: E 342 GLU cc_start: 0.7489 (tp30) cc_final: 0.7044 (tp30) REVERT: E 365 LEU cc_start: 0.8788 (pt) cc_final: 0.8383 (mp) REVERT: E 583 MET cc_start: 0.8677 (mtp) cc_final: 0.8464 (mtp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3232 time to fit residues: 99.3814 Evaluate side-chains 196 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.0070 chunk 133 optimal weight: 0.0270 chunk 110 optimal weight: 0.5980 chunk 61 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 128 optimal weight: 6.9990 overall best weight: 0.2134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 ASN E 284 ASN E 386 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6071 moved from start: 0.4414 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= 0.180 Angle : 0.669 9.161 16547 Z= 0.348 Chirality : 0.046 0.323 1896 Planarity : 0.004 0.053 1892 Dihedral : 19.475 164.980 2087 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.70 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.22), residues: 1319 helix: -1.22 (0.28), residues: 311 sheet: -1.02 (0.30), residues: 321 loop : -2.63 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 50 HIS 0.002 0.000 HIS E 329 PHE 0.028 0.002 PHE B 27 TYR 0.019 0.002 TYR B 196 ARG 0.007 0.001 ARG B 227 *********************** 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 220 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.273 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: 0.7187 (t0) cc_final: 0.6592 (t0) REVERT: A 29 ASN cc_start: 0.6749 (t0) cc_final: 0.6547 (m110) REVERT: A 49 ILE cc_start: 0.7173 (mt) cc_final: 0.5927 (mt) REVERT: A 182 MET cc_start: 0.3866 (mmm) cc_final: 0.3532 (mmm) REVERT: A 210 LYS cc_start: 0.8738 (ptmt) cc_final: 0.8257 (ptpt) REVERT: A 244 TRP cc_start: 0.6734 (m100) cc_final: 0.5713 (m100) REVERT: B 16 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7533 (ttm-80) REVERT: B 26 ASN cc_start: 0.7904 (t0) cc_final: 0.7698 (t0) REVERT: B 68 ILE cc_start: 0.8318 (mt) cc_final: 0.7965 (mp) REVERT: B 93 ASN cc_start: 0.7612 (p0) cc_final: 0.7387 (p0) REVERT: B 156 HIS cc_start: 0.6771 (p90) cc_final: 0.6280 (p-80) REVERT: B 218 PHE cc_start: 0.8103 (t80) cc_final: 0.7540 (t80) REVERT: C 187 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6284 (tm-30) REVERT: E 29 LEU cc_start: 0.7611 (tp) cc_final: 0.7323 (mm) REVERT: E 66 LEU cc_start: 0.7605 (mt) cc_final: 0.7301 (mt) REVERT: E 99 LYS cc_start: 0.7798 (tttt) cc_final: 0.7559 (tttt) REVERT: E 123 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6194 (tm-30) REVERT: E 251 MET cc_start: 0.7714 (mmm) cc_final: 0.7395 (mmm) REVERT: E 288 GLN cc_start: 0.7576 (mt0) cc_final: 0.7026 (mp10) REVERT: E 338 GLU cc_start: 0.6539 (tp30) cc_final: 0.5984 (tp30) REVERT: E 342 GLU cc_start: 0.7246 (tp30) cc_final: 0.6967 (tp30) REVERT: E 353 MET cc_start: 0.6417 (ptt) cc_final: 0.6177 (ptp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.3278 time to fit residues: 96.5721 Evaluate side-chains 183 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 288 GLN E 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12074 Z= 0.296 Angle : 0.742 13.504 16547 Z= 0.385 Chirality : 0.047 0.346 1896 Planarity : 0.004 0.051 1892 Dihedral : 19.438 163.614 2087 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 23.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.51 % Favored : 87.26 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.22), residues: 1319 helix: -1.33 (0.29), residues: 294 sheet: -1.17 (0.29), residues: 336 loop : -2.71 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP E 50 HIS 0.004 0.001 HIS B 156 PHE 0.032 0.003 PHE B 56 TYR 0.031 0.002 TYR B 196 ARG 0.007 0.001 ARG B 227 *********************** 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 219 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.234 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 24 ASP cc_start: 0.7270 (t0) cc_final: 0.6623 (t0) REVERT: A 89 ILE cc_start: 0.7693 (tt) cc_final: 0.7415 (tt) REVERT: A 91 LEU cc_start: 0.8197 (tp) cc_final: 0.7183 (pt) REVERT: A 116 LYS cc_start: 0.8377 (tptp) cc_final: 0.8094 (mtpp) REVERT: A 182 MET cc_start: 0.4382 (mmm) cc_final: 0.3919 (mmm) REVERT: B 26 ASN cc_start: 0.8056 (t0) cc_final: 0.7817 (t0) REVERT: B 93 ASN cc_start: 0.7822 (p0) cc_final: 0.7517 (p0) REVERT: B 145 GLU cc_start: 0.7468 (mm-30) cc_final: 0.6670 (mm-30) REVERT: B 156 HIS cc_start: 0.6909 (p90) cc_final: 0.6636 (p-80) REVERT: B 243 ARG cc_start: 0.7556 (tpp-160) cc_final: 0.7335 (tpp80) REVERT: C 78 LEU cc_start: 0.8000 (mt) cc_final: 0.7768 (mt) REVERT: C 112 ARG cc_start: 0.7324 (ptm-80) cc_final: 0.6926 (ptm-80) REVERT: E 1 MET cc_start: 0.6754 (tpt) cc_final: 0.6462 (tpt) REVERT: E 29 LEU cc_start: 0.7670 (tp) cc_final: 0.7452 (mm) REVERT: E 54 LEU cc_start: 0.8622 (mm) cc_final: 0.8389 (mt) REVERT: E 66 LEU cc_start: 0.7650 (mt) cc_final: 0.7373 (mt) REVERT: E 99 LYS cc_start: 0.8009 (tttt) cc_final: 0.7759 (tttt) REVERT: E 226 LYS cc_start: 0.5444 (tttt) cc_final: 0.4871 (tttt) REVERT: E 288 GLN cc_start: 0.7694 (mt0) cc_final: 0.7171 (mp10) REVERT: E 308 GLU cc_start: 0.7369 (tm-30) cc_final: 0.7082 (tm-30) REVERT: E 338 GLU cc_start: 0.6868 (tp30) cc_final: 0.6033 (tp30) REVERT: E 353 MET cc_start: 0.6614 (ptt) cc_final: 0.6370 (ptp) REVERT: E 433 LYS cc_start: 0.8255 (mtpt) cc_final: 0.8044 (mtpp) REVERT: E 583 MET cc_start: 0.8603 (mtm) cc_final: 0.8183 (mtm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3377 time to fit residues: 97.0843 Evaluate side-chains 187 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.0570 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 90 optimal weight: 0.0060 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN C 184 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS E 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12074 Z= 0.188 Angle : 0.672 10.671 16547 Z= 0.348 Chirality : 0.046 0.339 1896 Planarity : 0.004 0.052 1892 Dihedral : 19.460 166.033 2087 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.16 % Favored : 89.69 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.22), residues: 1319 helix: -1.12 (0.30), residues: 293 sheet: -1.17 (0.29), residues: 326 loop : -2.49 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 50 HIS 0.002 0.001 HIS E 329 PHE 0.022 0.002 PHE C 128 TYR 0.022 0.001 TYR B 196 ARG 0.010 0.001 ARG C 41 *********************** 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 214 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.206 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: 0.7528 (t0) cc_final: 0.7180 (t0) REVERT: A 91 LEU cc_start: 0.7860 (tp) cc_final: 0.7075 (pt) REVERT: A 114 TYR cc_start: 0.6617 (m-10) cc_final: 0.6410 (m-10) REVERT: A 182 MET cc_start: 0.4268 (mmm) cc_final: 0.3898 (mmm) REVERT: A 210 LYS cc_start: 0.8813 (ptmt) cc_final: 0.8365 (ptpt) REVERT: B 1 MET cc_start: 0.5124 (tpp) cc_final: 0.4802 (tpp) REVERT: B 26 ASN cc_start: 0.7949 (t0) cc_final: 0.7684 (t0) REVERT: B 93 ASN cc_start: 0.7582 (p0) cc_final: 0.7360 (p0) REVERT: B 133 GLN cc_start: 0.3927 (mm-40) cc_final: 0.3373 (mm-40) REVERT: B 156 HIS cc_start: 0.6772 (p90) cc_final: 0.6247 (p-80) REVERT: B 218 PHE cc_start: 0.8351 (t80) cc_final: 0.6726 (t80) REVERT: C 78 LEU cc_start: 0.8031 (mt) cc_final: 0.7710 (mt) REVERT: C 79 LYS cc_start: 0.7435 (pttt) cc_final: 0.7128 (pttm) REVERT: E 29 LEU cc_start: 0.7947 (tp) cc_final: 0.7685 (mt) REVERT: E 54 LEU cc_start: 0.8345 (mm) cc_final: 0.8137 (mt) REVERT: E 66 LEU cc_start: 0.7538 (mt) cc_final: 0.7248 (mt) REVERT: E 123 GLU cc_start: 0.7316 (tm-30) cc_final: 0.6575 (tm-30) REVERT: E 264 GLU cc_start: 0.5603 (tp30) cc_final: 0.5381 (tp30) REVERT: E 338 GLU cc_start: 0.6532 (tp30) cc_final: 0.6064 (tp30) REVERT: E 353 MET cc_start: 0.6390 (ptt) cc_final: 0.6141 (ptt) REVERT: E 583 MET cc_start: 0.8588 (mtm) cc_final: 0.8173 (mtm) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.3214 time to fit residues: 91.6657 Evaluate side-chains 188 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12074 Z= 0.220 Angle : 0.707 13.509 16547 Z= 0.365 Chirality : 0.046 0.345 1896 Planarity : 0.004 0.052 1892 Dihedral : 19.392 165.412 2087 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.99 % Favored : 88.78 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.22), residues: 1319 helix: -1.06 (0.30), residues: 297 sheet: -0.96 (0.29), residues: 336 loop : -2.56 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 50 HIS 0.004 0.001 HIS E 329 PHE 0.023 0.002 PHE B 128 TYR 0.020 0.001 TYR B 196 ARG 0.005 0.001 ARG B 35 *********************** 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 207 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 1.253 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: 0.7507 (t0) cc_final: 0.7161 (t0) REVERT: A 123 GLU cc_start: 0.8429 (pm20) cc_final: 0.7461 (pm20) REVERT: A 182 MET cc_start: 0.4503 (mmm) cc_final: 0.4021 (mmm) REVERT: A 210 LYS cc_start: 0.8822 (ptmt) cc_final: 0.8365 (ptpt) REVERT: B 26 ASN cc_start: 0.7754 (t0) cc_final: 0.7496 (t0) REVERT: B 93 ASN cc_start: 0.7647 (p0) cc_final: 0.7359 (p0) REVERT: B 145 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6430 (mt-10) REVERT: B 156 HIS cc_start: 0.6711 (p90) cc_final: 0.6448 (p-80) REVERT: C 112 ARG cc_start: 0.7170 (ptm-80) cc_final: 0.6889 (ptm-80) REVERT: E 1 MET cc_start: 0.6620 (tpt) cc_final: 0.5754 (tpt) REVERT: E 123 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6669 (tm-30) REVERT: E 304 GLU cc_start: 0.7526 (pm20) cc_final: 0.7274 (pm20) REVERT: E 308 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7181 (tm-30) REVERT: E 338 GLU cc_start: 0.6857 (tp30) cc_final: 0.6384 (tp30) REVERT: E 342 GLU cc_start: 0.6841 (pm20) cc_final: 0.6453 (pm20) REVERT: E 353 MET cc_start: 0.6548 (ptt) cc_final: 0.6213 (ptm) REVERT: E 583 MET cc_start: 0.8597 (mtm) cc_final: 0.8186 (mtm) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.3037 time to fit residues: 83.8259 Evaluate side-chains 180 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 126 optimal weight: 0.0370 chunk 109 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.5012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12074 Z= 0.195 Angle : 0.682 9.488 16547 Z= 0.352 Chirality : 0.045 0.344 1896 Planarity : 0.004 0.051 1892 Dihedral : 19.392 165.812 2087 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.54 % Favored : 89.23 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.23), residues: 1319 helix: -0.84 (0.30), residues: 290 sheet: -0.92 (0.29), residues: 338 loop : -2.52 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 50 HIS 0.003 0.001 HIS E 329 PHE 0.019 0.002 PHE B 27 TYR 0.022 0.001 TYR E 343 ARG 0.004 0.000 ARG B 35 ********************** 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 204 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.241 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: 0.7499 (t0) cc_final: 0.7110 (t0) REVERT: A 91 LEU cc_start: 0.7717 (tp) cc_final: 0.7165 (pt) REVERT: A 182 MET cc_start: 0.4294 (mmm) cc_final: 0.3829 (mmm) REVERT: A 210 LYS cc_start: 0.8818 (ptmt) cc_final: 0.8356 (ptpt) REVERT: B 26 ASN cc_start: 0.7563 (t0) cc_final: 0.7276 (t0) REVERT: B 67 ILE cc_start: 0.8622 (mp) cc_final: 0.8006 (mp) REVERT: B 68 ILE cc_start: 0.7638 (pt) cc_final: 0.6785 (pt) REVERT: B 127 GLU cc_start: 0.6600 (tm-30) cc_final: 0.6321 (tm-30) REVERT: B 145 GLU cc_start: 0.7339 (mm-30) cc_final: 0.7113 (mt-10) REVERT: B 156 HIS cc_start: 0.6735 (p90) cc_final: 0.6428 (p-80) REVERT: C 1 MET cc_start: 0.5981 (tmm) cc_final: 0.5726 (ttm) REVERT: E 1 MET cc_start: 0.6594 (tpt) cc_final: 0.5654 (tpt) REVERT: E 29 LEU cc_start: 0.7824 (tp) cc_final: 0.7609 (mt) REVERT: E 53 PHE cc_start: 0.6834 (p90) cc_final: 0.6544 (p90) REVERT: E 54 LEU cc_start: 0.8274 (mm) cc_final: 0.8053 (mt) REVERT: E 123 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6965 (tm-30) REVERT: E 140 ARG cc_start: 0.7259 (mmt180) cc_final: 0.7007 (mmt-90) REVERT: E 304 GLU cc_start: 0.7530 (pm20) cc_final: 0.7297 (pm20) REVERT: E 308 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7255 (tm-30) REVERT: E 338 GLU cc_start: 0.6730 (tp30) cc_final: 0.6462 (tp30) REVERT: E 342 GLU cc_start: 0.6835 (pm20) cc_final: 0.6370 (pm20) REVERT: E 353 MET cc_start: 0.6521 (ptt) cc_final: 0.6153 (ptm) REVERT: E 400 PHE cc_start: 0.4472 (m-80) cc_final: 0.4033 (m-80) REVERT: E 583 MET cc_start: 0.8594 (mtm) cc_final: 0.8171 (mtm) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.3081 time to fit residues: 83.8369 Evaluate side-chains 176 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 112 optimal weight: 0.0970 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 96 optimal weight: 0.0980 chunk 6 optimal weight: 0.2980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100 ASN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.194683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.166610 restraints weight = 26413.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.170478 restraints weight = 17746.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.173172 restraints weight = 12922.482| |-----------------------------------------------------------------------------| r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4420 r_free = 0.4420 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.5209 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= 0.175 Angle : 0.670 8.886 16547 Z= 0.346 Chirality : 0.045 0.340 1896 Planarity : 0.004 0.053 1892 Dihedral : 19.346 165.846 2087 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.86 % Favored : 89.92 % 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 : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.23), residues: 1319 helix: -0.78 (0.30), residues: 290 sheet: -0.91 (0.29), residues: 342 loop : -2.47 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.003 0.001 HIS E 329 PHE 0.021 0.002 PHE C 128 TYR 0.025 0.001 TYR E 343 ARG 0.009 0.000 ARG E 164 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2737.01 seconds wall clock time: 50 minutes 3.39 seconds (3003.39 seconds total)