Starting phenix.real_space_refine on Sat Oct 12 07:13:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/10_2024/7rpx_24625.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/10_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_24625/10_2024/7rpx_24625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/10_2024/7rpx_24625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/10_2024/7rpx_24625.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rpx_24625/10_2024/7rpx_24625.cif" } 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. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/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: 6.71, per 1000 atoms: 0.57 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: 3.07 Conformation dependent library (CDL) restraints added in 1.5 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: 4.26 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 142 through 154 removed outlier: 4.351A pdb=" N LEU A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 154 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'B' and resid 7 through 17 removed outlier: 3.973A pdb=" N SER B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 13 " --> pdb=" O VAL B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 20 No H-bonds generated for 'chain 'B' and resid 18 through 20' Processing helix chain 'B' and resid 71 through 78 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 136 through 147 removed outlier: 4.263A pdb=" N ALA B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASP B 141 " --> pdb=" O ILE B 137 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.502A pdb=" N ASN B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 14 Processing helix chain 'C' and resid 15 through 20 removed outlier: 4.445A pdb=" N ARG C 20 " --> pdb=" O GLN C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 77 Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.877A pdb=" N SER C 147 " --> pdb=" O ILE C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 202 Processing helix chain 'C' and resid 204 through 211 removed outlier: 3.842A pdb=" N LEU C 207 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 208 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS C 209 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 210 " --> pdb=" O LEU C 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 21 through 30 removed outlier: 4.054A pdb=" N LEU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 42 removed outlier: 4.242A pdb=" N ASP E 39 " --> pdb=" O LYS E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 removed outlier: 3.572A pdb=" N GLN E 46 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 77 through 89 removed outlier: 4.191A pdb=" N VAL E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 120 through 134 removed outlier: 3.508A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 153 removed outlier: 3.559A pdb=" N LEU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 168 removed outlier: 3.530A pdb=" N VAL E 166 " --> pdb=" O LEU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 187 removed outlier: 3.677A pdb=" N VAL E 179 " --> pdb=" O GLY E 175 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP E 181 " --> pdb=" O ALA E 177 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 193 through 204 removed outlier: 4.203A pdb=" N LEU E 203 " --> pdb=" O ARG E 199 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG E 204 " --> pdb=" O ALA E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 Processing helix chain 'E' and resid 218 through 223 Processing helix chain 'E' and resid 289 through 297 removed outlier: 4.047A pdb=" N VAL E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP E 294 " --> pdb=" O PRO E 290 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N TYR E 295 " --> pdb=" O ASP E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 329 through 332 removed outlier: 4.015A pdb=" N ARG E 332 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 329 through 332' Processing helix chain 'E' and resid 335 through 340 removed outlier: 3.631A pdb=" N ALA E 339 " --> pdb=" O ASP E 335 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 335 through 340' Processing helix chain 'E' and resid 392 through 398 removed outlier: 3.743A pdb=" N LYS E 397 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER E 398 " --> pdb=" O ASP E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 404 Processing helix chain 'E' and resid 490 through 504 removed outlier: 3.764A pdb=" N GLN E 498 " --> pdb=" O LEU E 494 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS E 499 " --> pdb=" O ASP E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 574 Processing helix chain 'E' and resid 576 through 587 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 3.604A pdb=" N ILE A 4 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS A 110 " --> pdb=" O GLU C 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.527A pdb=" N ARG A 51 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 233 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 243 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 231 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 245 " --> pdb=" O MET A 229 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 229 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY A 224 " --> pdb=" O PRO A 228 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 134 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 201 removed outlier: 4.155A pdb=" N MET A 157 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A 179 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA A 170 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR A 177 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 178 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 removed outlier: 4.011A pdb=" N LEU B 88 " --> pdb=" O VAL B 5 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 67 removed outlier: 3.868A pdb=" N GLU B 66 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN B 26 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B 37 " --> pdb=" O ASN B 26 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 28 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE B 34 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 47 " --> pdb=" O GLY B 38 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP B 48 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ASP B 237 " --> pdb=" O ASP B 48 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 213 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 216 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 193 through 197 removed outlier: 3.681A pdb=" N ILE B 155 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 152 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 167 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS B 156 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 163 " --> pdb=" O HIS B 156 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 108 " --> pdb=" O LYS B 174 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 107 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL C 111 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU C 58 " --> pdb=" O VAL C 4 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 28 through 29 removed outlier: 3.835A pdb=" N LYS C 28 " --> pdb=" O GLU C 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 163 through 165 Processing sheet with id=AB1, first strand: chain 'E' and resid 256 through 257 removed outlier: 3.601A pdb=" N VAL E 257 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE E 388 " --> pdb=" O VAL E 257 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 265 through 266 removed outlier: 6.621A pdb=" N GLU E 308 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL E 312 " --> pdb=" O ASN E 346 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N LYS E 383 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL E 347 " --> pdb=" O LYS E 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 354 through 355 removed outlier: 3.828A pdb=" N TYR E 355 " --> pdb=" O VAL E 358 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 505 through 506 removed outlier: 3.818A pdb=" N TRP E 522 " --> pdb=" O ARG E 506 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE E 521 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY E 453 " --> pdb=" O ILE E 521 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL E 451 " --> pdb=" O VAL E 523 " (cutoff:3.500A) removed outlier: 9.952A pdb=" N LEU E 448 " --> pdb=" O TYR E 472 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N TYR E 472 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N VAL E 450 " --> pdb=" O ALA E 470 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA E 470 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY E 452 " --> pdb=" O LEU E 468 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS E 483 " --> pdb=" O MET E 469 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ALA E 471 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER E 481 " --> pdb=" O ALA E 471 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN E 473 " --> pdb=" O PHE E 479 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE E 479 " --> pdb=" O ASN E 473 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE E 479 " --> pdb=" O ASN E 514 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 505 through 506 removed outlier: 3.818A pdb=" N TRP E 522 " --> pdb=" O ARG E 506 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE E 521 " --> pdb=" O GLY E 453 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLY E 453 " --> pdb=" O ILE E 521 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL E 451 " --> pdb=" O VAL E 523 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 564 " --> pdb=" O GLU E 530 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE E 532 " --> pdb=" O PHE E 562 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N PHE E 562 " --> pdb=" O ILE E 532 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 536 through 539 311 hydrogen bonds defined for protein. 834 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 3.51 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: 0.00 - 2.12: 16346 2.12 - 4.24: 188 4.24 - 6.37: 10 6.37 - 8.49: 1 8.49 - 10.61: 2 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 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: 0.440 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.600 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- 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 : 1.426 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: 0.3402 time to fit residues: 133.3797 Evaluate side-chains 221 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 215 time to evaluate : 1.241 ------------------------------------------------------------------------------- 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: 0.0000 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 108 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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** E 288 GLN E 386 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12074 Z= 0.244 Angle : 0.693 9.611 16547 Z= 0.371 Chirality : 0.048 0.227 1896 Planarity : 0.005 0.053 1892 Dihedral : 19.349 160.160 2087 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.46 % Favored : 89.31 % Rotamer: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % 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: -2.74 (0.22), residues: 1319 helix: -1.31 (0.28), residues: 308 sheet: -0.93 (0.29), residues: 337 loop : -2.59 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 431 HIS 0.002 0.001 HIS B 156 PHE 0.027 0.002 PHE E 400 TYR 0.023 0.002 TYR B 13 ARG 0.005 0.001 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 251 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 1.189 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: 0.6719 (t0) cc_final: 0.5998 (t0) REVERT: A 164 ASP cc_start: 0.7696 (t0) cc_final: 0.6248 (t0) REVERT: A 165 LYS cc_start: 0.8653 (pttm) cc_final: 0.7999 (pttm) REVERT: A 182 MET cc_start: 0.3819 (mmm) cc_final: 0.3598 (mmm) REVERT: A 183 LYS cc_start: 0.9095 (tttt) cc_final: 0.8697 (mmtm) REVERT: A 184 ASP cc_start: 0.7602 (t0) cc_final: 0.7120 (t0) REVERT: A 185 LYS cc_start: 0.8154 (mmtm) cc_final: 0.7825 (mmtm) REVERT: A 210 LYS cc_start: 0.8764 (ptmt) cc_final: 0.8053 (ptpp) REVERT: A 244 TRP cc_start: 0.6929 (m100) cc_final: 0.6564 (m100) REVERT: B 59 PHE cc_start: 0.7388 (t80) cc_final: 0.7185 (t80) REVERT: B 156 HIS cc_start: 0.6983 (p90) cc_final: 0.6522 (p-80) REVERT: B 213 SER cc_start: 0.6287 (t) cc_final: 0.5982 (p) REVERT: C 78 LEU cc_start: 0.7898 (mt) cc_final: 0.7688 (mt) REVERT: C 230 MET cc_start: 0.0844 (mtp) cc_final: 0.0582 (mtp) REVERT: E 99 LYS cc_start: 0.7821 (tttt) cc_final: 0.7564 (tttt) REVERT: E 123 GLU cc_start: 0.6325 (tm-30) cc_final: 0.5725 (tm-30) REVERT: E 160 LYS cc_start: 0.7293 (mttt) cc_final: 0.6925 (ptpp) REVERT: E 338 GLU cc_start: 0.6758 (tp30) cc_final: 0.6550 (tp30) REVERT: E 342 GLU cc_start: 0.7042 (tp30) cc_final: 0.6677 (tm-30) REVERT: E 583 MET cc_start: 0.8689 (mtp) cc_final: 0.8465 (mtp) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.3348 time to fit residues: 110.3266 Evaluate side-chains 204 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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: 0.2980 chunk 38 optimal weight: 0.9990 chunk 104 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 135 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 284 ASN E 288 GLN E 386 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12074 Z= 0.216 Angle : 0.653 9.409 16547 Z= 0.347 Chirality : 0.046 0.201 1896 Planarity : 0.004 0.053 1892 Dihedral : 19.303 162.648 2087 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.69 % Favored : 89.08 % Rotamer: Outliers : 0.34 % Allowed : 3.60 % Favored : 96.06 % 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: -2.74 (0.22), residues: 1319 helix: -1.16 (0.29), residues: 302 sheet: -0.97 (0.29), residues: 333 loop : -2.64 (0.22), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 244 HIS 0.002 0.001 HIS E 510 PHE 0.021 0.002 PHE B 27 TYR 0.020 0.002 TYR C 200 ARG 0.005 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 244 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 240 time to evaluate : 1.323 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: 0.7015 (t0) cc_final: 0.6329 (t0) REVERT: A 164 ASP cc_start: 0.7754 (t0) cc_final: 0.6027 (t0) REVERT: A 165 LYS cc_start: 0.8656 (pttm) cc_final: 0.8429 (pttm) REVERT: A 182 MET cc_start: 0.3808 (mmm) cc_final: 0.3481 (mmm) REVERT: A 183 LYS cc_start: 0.8603 (tttt) cc_final: 0.8390 (mmtm) REVERT: B 59 PHE cc_start: 0.7362 (t80) cc_final: 0.7047 (t80) REVERT: B 68 ILE cc_start: 0.7983 (mp) cc_final: 0.7670 (mp) REVERT: B 156 HIS cc_start: 0.6877 (p90) cc_final: 0.6431 (p-80) REVERT: B 158 LYS cc_start: 0.8051 (tptp) cc_final: 0.7818 (tppt) REVERT: B 218 PHE cc_start: 0.8284 (t80) cc_final: 0.7212 (t80) REVERT: B 227 ARG cc_start: 0.5847 (tpp80) cc_final: 0.5581 (mmm160) REVERT: C 66 LYS cc_start: 0.6986 (tttt) cc_final: 0.6714 (ttpt) REVERT: C 112 ARG cc_start: 0.7142 (ptm-80) cc_final: 0.6801 (ptm-80) REVERT: C 187 GLU cc_start: 0.6102 (tm-30) cc_final: 0.5688 (tm-30) REVERT: C 230 MET cc_start: 0.0650 (mtp) cc_final: 0.0340 (ttm) REVERT: E 54 LEU cc_start: 0.8534 (mm) cc_final: 0.8170 (mt) REVERT: E 99 LYS cc_start: 0.7782 (tttt) cc_final: 0.7572 (tttt) REVERT: E 123 GLU cc_start: 0.6760 (tm-30) cc_final: 0.6094 (tm-30) REVERT: E 140 ARG cc_start: 0.6706 (mpt180) cc_final: 0.6453 (mmt-90) REVERT: E 143 LYS cc_start: 0.6770 (mtmm) cc_final: 0.6441 (mtmm) REVERT: E 338 GLU cc_start: 0.6591 (tp30) cc_final: 0.6062 (tp30) REVERT: E 342 GLU cc_start: 0.7088 (tp30) cc_final: 0.6715 (tm-30) REVERT: E 414 LYS cc_start: 0.7422 (mmmt) cc_final: 0.7118 (mmmt) REVERT: E 430 LEU cc_start: 0.8247 (tt) cc_final: 0.7893 (tp) REVERT: E 583 MET cc_start: 0.8679 (mtp) cc_final: 0.8471 (mtp) outliers start: 4 outliers final: 0 residues processed: 243 average time/residue: 0.3339 time to fit residues: 106.5177 Evaluate side-chains 200 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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: 10.0000 chunk 94 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 40.0000 chunk 119 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12074 Z= 0.302 Angle : 0.721 11.612 16547 Z= 0.380 Chirality : 0.047 0.213 1896 Planarity : 0.004 0.052 1892 Dihedral : 19.448 163.231 2087 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.36 % Favored : 87.41 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % 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: -2.87 (0.22), residues: 1319 helix: -1.47 (0.28), residues: 303 sheet: -0.97 (0.29), residues: 335 loop : -2.66 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 431 HIS 0.005 0.001 HIS B 156 PHE 0.023 0.003 PHE B 27 TYR 0.021 0.002 TYR A 6 ARG 0.009 0.001 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 234 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7178 (t0) cc_final: 0.6544 (t0) REVERT: A 76 LYS cc_start: 0.7518 (tptt) cc_final: 0.7212 (tptp) REVERT: A 116 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7630 (mtpp) REVERT: A 165 LYS cc_start: 0.8792 (pttm) cc_final: 0.8589 (pttm) REVERT: A 182 MET cc_start: 0.4493 (mmm) cc_final: 0.4063 (mmm) REVERT: B 145 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6759 (mm-30) REVERT: B 156 HIS cc_start: 0.6994 (p90) cc_final: 0.6434 (p-80) REVERT: C 66 LYS cc_start: 0.7318 (tttt) cc_final: 0.6849 (ttpt) REVERT: C 78 LEU cc_start: 0.8006 (mt) cc_final: 0.7742 (mt) REVERT: C 79 LYS cc_start: 0.7837 (pttm) cc_final: 0.7509 (pttp) REVERT: C 115 GLU cc_start: 0.8235 (tp30) cc_final: 0.7786 (tp30) REVERT: C 187 GLU cc_start: 0.6270 (tm-30) cc_final: 0.5904 (tm-30) REVERT: C 230 MET cc_start: 0.0887 (mtp) cc_final: 0.0616 (ttm) REVERT: E 64 LYS cc_start: 0.7879 (ttmt) cc_final: 0.7625 (mtpp) REVERT: E 123 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6799 (tm-30) REVERT: E 288 GLN cc_start: 0.7679 (mt0) cc_final: 0.7101 (mp10) REVERT: E 338 GLU cc_start: 0.6786 (tp30) cc_final: 0.6196 (tp30) REVERT: E 342 GLU cc_start: 0.7231 (tp30) cc_final: 0.6777 (tm-30) REVERT: E 353 MET cc_start: 0.6351 (ptp) cc_final: 0.6099 (ptp) REVERT: E 583 MET cc_start: 0.8677 (mtp) cc_final: 0.8475 (mtp) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.3240 time to fit residues: 100.8530 Evaluate side-chains 200 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.176 ------------------------------------------------------------------------------- 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: 1.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12074 Z= 0.257 Angle : 0.690 9.659 16547 Z= 0.364 Chirality : 0.046 0.180 1896 Planarity : 0.004 0.052 1892 Dihedral : 19.459 164.837 2087 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.37 % Favored : 88.40 % Rotamer: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.87 (0.22), residues: 1319 helix: -1.50 (0.28), residues: 295 sheet: -0.93 (0.29), residues: 335 loop : -2.66 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 429 HIS 0.003 0.001 HIS B 156 PHE 0.028 0.002 PHE C 128 TYR 0.022 0.002 TYR E 85 ARG 0.004 0.001 ARG B 107 *********************** 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 225 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.258 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: 0.7338 (t0) cc_final: 0.6704 (t0) REVERT: A 76 LYS cc_start: 0.7742 (tptt) cc_final: 0.7425 (mmmt) REVERT: A 116 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7634 (mtpp) REVERT: A 164 ASP cc_start: 0.7867 (t70) cc_final: 0.6168 (t0) REVERT: A 165 LYS cc_start: 0.8912 (pttm) cc_final: 0.8652 (pttm) REVERT: A 182 MET cc_start: 0.4349 (mmm) cc_final: 0.3877 (mmm) REVERT: A 210 LYS cc_start: 0.8731 (ptmt) cc_final: 0.8219 (ptpt) REVERT: B 68 ILE cc_start: 0.8273 (mp) cc_final: 0.7782 (mp) REVERT: B 145 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6933 (mm-30) REVERT: B 156 HIS cc_start: 0.6930 (p90) cc_final: 0.6362 (p-80) REVERT: C 78 LEU cc_start: 0.8045 (mt) cc_final: 0.7773 (mt) REVERT: C 187 GLU cc_start: 0.6332 (tm-30) cc_final: 0.5913 (tm-30) REVERT: C 230 MET cc_start: 0.0944 (mtp) cc_final: 0.0653 (ttm) REVERT: E 53 PHE cc_start: 0.7179 (p90) cc_final: 0.6676 (p90) REVERT: E 54 LEU cc_start: 0.8533 (mm) cc_final: 0.8218 (mt) REVERT: E 66 LEU cc_start: 0.7448 (mm) cc_final: 0.7199 (mm) REVERT: E 123 GLU cc_start: 0.6814 (tm-30) cc_final: 0.6474 (tm-30) REVERT: E 180 LEU cc_start: 0.7614 (mt) cc_final: 0.7386 (mt) REVERT: E 181 ASP cc_start: 0.7026 (m-30) cc_final: 0.6808 (t0) REVERT: E 251 MET cc_start: 0.7901 (mmm) cc_final: 0.7648 (mmm) REVERT: E 258 ASP cc_start: 0.6233 (p0) cc_final: 0.5947 (p0) REVERT: E 288 GLN cc_start: 0.7675 (mt0) cc_final: 0.7003 (mp10) REVERT: E 338 GLU cc_start: 0.6775 (tp30) cc_final: 0.6207 (tp30) REVERT: E 342 GLU cc_start: 0.7261 (tp30) cc_final: 0.6903 (tp30) REVERT: E 430 LEU cc_start: 0.8216 (tt) cc_final: 0.8001 (tt) REVERT: E 583 MET cc_start: 0.8680 (mtp) cc_final: 0.8476 (mtp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3269 time to fit residues: 97.5631 Evaluate side-chains 190 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 133 optimal weight: 50.0000 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 128 optimal weight: 20.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12074 Z= 0.241 Angle : 0.685 8.541 16547 Z= 0.361 Chirality : 0.046 0.191 1896 Planarity : 0.004 0.053 1892 Dihedral : 19.487 165.646 2087 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.52 % Favored : 88.17 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -2.90 (0.22), residues: 1319 helix: -1.56 (0.28), residues: 302 sheet: -0.98 (0.29), residues: 340 loop : -2.64 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 431 HIS 0.004 0.001 HIS A 39 PHE 0.022 0.002 PHE B 27 TYR 0.018 0.002 TYR A 177 ARG 0.004 0.000 ARG C 83 *********************** 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 219 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7268 (t0) cc_final: 0.6676 (t0) REVERT: A 29 ASN cc_start: 0.7090 (t0) cc_final: 0.6782 (m110) REVERT: A 49 ILE cc_start: 0.7206 (mt) cc_final: 0.6698 (mt) REVERT: A 76 LYS cc_start: 0.7659 (tptt) cc_final: 0.7443 (mmmt) REVERT: A 116 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7642 (mtpp) REVERT: A 182 MET cc_start: 0.4512 (mmm) cc_final: 0.4061 (mmm) REVERT: A 210 LYS cc_start: 0.8731 (ptmt) cc_final: 0.8202 (ptpt) REVERT: A 244 TRP cc_start: 0.6840 (m100) cc_final: 0.6137 (m100) REVERT: B 156 HIS cc_start: 0.6762 (p90) cc_final: 0.6514 (p-80) REVERT: B 214 MET cc_start: 0.6767 (ttm) cc_final: 0.6397 (ttm) REVERT: C 1 MET cc_start: 0.6298 (tmm) cc_final: 0.6082 (ttm) REVERT: C 78 LEU cc_start: 0.8032 (mt) cc_final: 0.7823 (mt) REVERT: C 230 MET cc_start: 0.0871 (mtp) cc_final: 0.0600 (ttm) REVERT: E 53 PHE cc_start: 0.7118 (p90) cc_final: 0.6651 (p90) REVERT: E 54 LEU cc_start: 0.8439 (mm) cc_final: 0.8153 (mt) REVERT: E 99 LYS cc_start: 0.7969 (tttt) cc_final: 0.7706 (tttt) REVERT: E 123 GLU cc_start: 0.7322 (tm-30) cc_final: 0.6939 (tm-30) REVERT: E 180 LEU cc_start: 0.7619 (mt) cc_final: 0.7418 (mt) REVERT: E 181 ASP cc_start: 0.7185 (m-30) cc_final: 0.6939 (t0) REVERT: E 258 ASP cc_start: 0.6205 (p0) cc_final: 0.5939 (p0) REVERT: E 288 GLN cc_start: 0.7595 (mt0) cc_final: 0.6983 (mp10) REVERT: E 338 GLU cc_start: 0.6862 (tp30) cc_final: 0.6334 (tp30) REVERT: E 342 GLU cc_start: 0.7375 (tp30) cc_final: 0.6927 (tp30) REVERT: E 583 MET cc_start: 0.8661 (mtp) cc_final: 0.8416 (mtp) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.3331 time to fit residues: 96.2163 Evaluate side-chains 193 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 1.402 ------------------------------------------------------------------------------- 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: 3.9990 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 50.0000 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 0.0670 chunk 82 optimal weight: 0.7980 overall best weight: 1.4322 ------------------------------------------------------------------------------- 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 386 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 moved from start: 0.4642 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= 0.265 Angle : 0.703 8.966 16547 Z= 0.371 Chirality : 0.047 0.206 1896 Planarity : 0.004 0.052 1892 Dihedral : 19.539 166.256 2087 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.30 % Allowed : 11.68 % Favored : 88.02 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % 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: -2.93 (0.22), residues: 1319 helix: -1.48 (0.28), residues: 294 sheet: -1.17 (0.29), residues: 340 loop : -2.61 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 431 HIS 0.005 0.001 HIS A 39 PHE 0.028 0.003 PHE E 165 TYR 0.020 0.002 TYR A 177 ARG 0.006 0.000 ARG A 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.279 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: 0.7233 (t0) cc_final: 0.6669 (t0) REVERT: A 50 MET cc_start: 0.4144 (tpt) cc_final: 0.3398 (tmm) REVERT: A 76 LYS cc_start: 0.7850 (tptt) cc_final: 0.7378 (tptp) REVERT: A 116 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7662 (mtpp) REVERT: A 123 GLU cc_start: 0.8433 (pm20) cc_final: 0.8056 (pm20) REVERT: A 164 ASP cc_start: 0.8100 (m-30) cc_final: 0.7528 (t0) REVERT: A 165 LYS cc_start: 0.8697 (pttm) cc_final: 0.8346 (ptpt) REVERT: A 182 MET cc_start: 0.4633 (mmm) cc_final: 0.4103 (mmm) REVERT: A 183 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8031 (mmmt) REVERT: A 210 LYS cc_start: 0.8778 (ptmt) cc_final: 0.8196 (ptpt) REVERT: B 133 GLN cc_start: 0.3662 (mm-40) cc_final: 0.3253 (mm-40) REVERT: B 156 HIS cc_start: 0.6698 (p90) cc_final: 0.6435 (p-80) REVERT: C 112 ARG cc_start: 0.7308 (ptm-80) cc_final: 0.6956 (ptm-80) REVERT: C 187 GLU cc_start: 0.6470 (tm-30) cc_final: 0.5627 (tm-30) REVERT: C 230 MET cc_start: 0.0876 (mtp) cc_final: 0.0668 (ttm) REVERT: E 29 LEU cc_start: 0.7772 (tp) cc_final: 0.7454 (mm) REVERT: E 53 PHE cc_start: 0.7043 (p90) cc_final: 0.6583 (p90) REVERT: E 54 LEU cc_start: 0.8544 (mm) cc_final: 0.8264 (mt) REVERT: E 66 LEU cc_start: 0.7442 (mm) cc_final: 0.7195 (mm) REVERT: E 99 LYS cc_start: 0.8020 (tttt) cc_final: 0.7727 (tttt) REVERT: E 123 GLU cc_start: 0.7552 (tm-30) cc_final: 0.7205 (tm-30) REVERT: E 258 ASP cc_start: 0.6385 (p0) cc_final: 0.6039 (p0) REVERT: E 288 GLN cc_start: 0.7610 (mt0) cc_final: 0.7011 (mp10) REVERT: E 338 GLU cc_start: 0.6875 (tp30) cc_final: 0.6068 (tp30) REVERT: E 583 MET cc_start: 0.8666 (mtp) cc_final: 0.8425 (mtp) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.3489 time to fit residues: 103.3789 Evaluate side-chains 191 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.954 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.4784 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= 0.209 Angle : 0.677 10.118 16547 Z= 0.354 Chirality : 0.045 0.178 1896 Planarity : 0.004 0.051 1892 Dihedral : 19.518 166.905 2087 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.69 % Favored : 89.08 % 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 (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: -2.81 (0.22), residues: 1319 helix: -1.42 (0.29), residues: 300 sheet: -0.99 (0.30), residues: 322 loop : -2.55 (0.22), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 431 HIS 0.003 0.001 HIS A 39 PHE 0.023 0.002 PHE B 27 TYR 0.015 0.002 TYR E 422 ARG 0.004 0.000 ARG B 227 *********************** 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 218 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.379 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: 0.7270 (t0) cc_final: 0.6939 (t0) REVERT: A 51 ARG cc_start: 0.6221 (tmm-80) cc_final: 0.5422 (tmm-80) REVERT: A 76 LYS cc_start: 0.7779 (tptt) cc_final: 0.7326 (tptp) REVERT: A 116 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7655 (mtpp) REVERT: A 164 ASP cc_start: 0.8092 (m-30) cc_final: 0.7466 (t0) REVERT: A 182 MET cc_start: 0.4368 (mmm) cc_final: 0.4092 (mmm) REVERT: A 183 LYS cc_start: 0.8405 (mmtm) cc_final: 0.7948 (mmmt) REVERT: A 210 LYS cc_start: 0.8778 (ptmt) cc_final: 0.8227 (ptpt) REVERT: B 156 HIS cc_start: 0.6717 (p90) cc_final: 0.6515 (p-80) REVERT: C 78 LEU cc_start: 0.8070 (mt) cc_final: 0.7837 (mt) REVERT: C 112 ARG cc_start: 0.7120 (ptm-80) cc_final: 0.6827 (ptm-80) REVERT: C 230 MET cc_start: 0.0751 (mtp) cc_final: 0.0499 (ttm) REVERT: E 29 LEU cc_start: 0.7690 (tp) cc_final: 0.7484 (mt) REVERT: E 53 PHE cc_start: 0.6983 (p90) cc_final: 0.6417 (p90) REVERT: E 66 LEU cc_start: 0.7415 (mm) cc_final: 0.7046 (mm) REVERT: E 99 LYS cc_start: 0.7919 (tttt) cc_final: 0.7688 (tttt) REVERT: E 160 LYS cc_start: 0.6695 (ptpp) cc_final: 0.6329 (mptt) REVERT: E 258 ASP cc_start: 0.6143 (p0) cc_final: 0.5751 (p0) REVERT: E 288 GLN cc_start: 0.7561 (mt0) cc_final: 0.7006 (mp10) REVERT: E 338 GLU cc_start: 0.6676 (tp30) cc_final: 0.5780 (tp30) REVERT: E 353 MET cc_start: 0.6638 (ptt) cc_final: 0.6433 (ptp) REVERT: E 433 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7603 (mtpp) REVERT: E 583 MET cc_start: 0.8670 (mtp) cc_final: 0.8419 (mtp) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3452 time to fit residues: 99.9572 Evaluate side-chains 187 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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: 7.9990 chunk 116 optimal weight: 0.0470 chunk 123 optimal weight: 20.0000 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 97 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 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: 0.6101 moved from start: 0.4951 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= 0.196 Angle : 0.673 9.110 16547 Z= 0.352 Chirality : 0.046 0.205 1896 Planarity : 0.004 0.052 1892 Dihedral : 19.465 166.901 2087 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.39 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -2.67 (0.22), residues: 1319 helix: -1.09 (0.30), residues: 288 sheet: -0.95 (0.29), residues: 326 loop : -2.54 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 431 HIS 0.003 0.001 HIS A 39 PHE 0.026 0.002 PHE A 15 TYR 0.016 0.001 TYR E 422 ARG 0.005 0.000 ARG A 51 *********************** 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 203 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 1.332 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: 0.7255 (t0) cc_final: 0.6918 (t0) REVERT: A 47 MET cc_start: 0.3724 (ptt) cc_final: 0.3109 (ppp) REVERT: A 49 ILE cc_start: 0.6881 (mt) cc_final: 0.6370 (pt) REVERT: A 182 MET cc_start: 0.4158 (mmm) cc_final: 0.3846 (mmm) REVERT: A 210 LYS cc_start: 0.8810 (ptmt) cc_final: 0.8231 (ptpt) REVERT: B 26 ASN cc_start: 0.8006 (t0) cc_final: 0.7743 (t0) REVERT: B 156 HIS cc_start: 0.6666 (p90) cc_final: 0.6440 (p-80) REVERT: C 112 ARG cc_start: 0.7221 (ptm-80) cc_final: 0.6928 (ptm-80) REVERT: C 230 MET cc_start: 0.1015 (mtp) cc_final: 0.0802 (ttm) REVERT: E 54 LEU cc_start: 0.8575 (mm) cc_final: 0.8358 (mt) REVERT: E 66 LEU cc_start: 0.7204 (mm) cc_final: 0.6819 (mm) REVERT: E 99 LYS cc_start: 0.7801 (tttt) cc_final: 0.7580 (tttt) REVERT: E 123 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6238 (tm-30) REVERT: E 251 MET cc_start: 0.7065 (mmm) cc_final: 0.6859 (mmm) REVERT: E 258 ASP cc_start: 0.6257 (p0) cc_final: 0.5780 (p0) REVERT: E 288 GLN cc_start: 0.7531 (mt0) cc_final: 0.7122 (mp10) REVERT: E 338 GLU cc_start: 0.6671 (tp30) cc_final: 0.6207 (tp30) REVERT: E 583 MET cc_start: 0.8686 (mtp) cc_final: 0.8440 (mtp) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.3391 time to fit residues: 92.6177 Evaluate side-chains 176 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 137 optimal weight: 9.9990 chunk 126 optimal weight: 30.0000 chunk 109 optimal weight: 0.0670 chunk 11 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 67 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN C 184 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.5118 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= 0.186 Angle : 0.676 9.074 16547 Z= 0.354 Chirality : 0.046 0.269 1896 Planarity : 0.004 0.051 1892 Dihedral : 19.415 166.810 2087 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.70 % Favored : 90.07 % 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: -2.62 (0.22), residues: 1319 helix: -1.06 (0.30), residues: 293 sheet: -0.85 (0.29), residues: 328 loop : -2.55 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 431 HIS 0.003 0.001 HIS A 39 PHE 0.020 0.002 PHE C 128 TYR 0.016 0.001 TYR C 200 ARG 0.003 0.000 ARG C 83 ********************** 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 202 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.351 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: 0.7247 (t0) cc_final: 0.6906 (t0) REVERT: A 26 ILE cc_start: 0.7191 (pt) cc_final: 0.6984 (pt) REVERT: A 47 MET cc_start: 0.3707 (ptt) cc_final: 0.3177 (ppp) REVERT: A 49 ILE cc_start: 0.6771 (mt) cc_final: 0.6457 (pt) REVERT: A 164 ASP cc_start: 0.8208 (m-30) cc_final: 0.7598 (t0) REVERT: A 182 MET cc_start: 0.4261 (mmm) cc_final: 0.3790 (mmm) REVERT: A 210 LYS cc_start: 0.8792 (ptmt) cc_final: 0.8199 (ptpt) REVERT: A 241 MET cc_start: 0.4307 (mmp) cc_final: 0.3895 (mmt) REVERT: B 26 ASN cc_start: 0.8084 (t0) cc_final: 0.7867 (t0) REVERT: B 156 HIS cc_start: 0.6644 (p90) cc_final: 0.6394 (p-80) REVERT: C 230 MET cc_start: 0.0961 (mtp) cc_final: 0.0759 (ttm) REVERT: E 66 LEU cc_start: 0.7204 (mm) cc_final: 0.6894 (mm) REVERT: E 123 GLU cc_start: 0.7086 (tm-30) cc_final: 0.5766 (tm-30) REVERT: E 251 MET cc_start: 0.7240 (mmm) cc_final: 0.7028 (mmm) REVERT: E 258 ASP cc_start: 0.6224 (p0) cc_final: 0.5789 (p0) REVERT: E 288 GLN cc_start: 0.7505 (mt0) cc_final: 0.7167 (mt0) REVERT: E 338 GLU cc_start: 0.6906 (tp30) cc_final: 0.6490 (tp30) REVERT: E 342 GLU cc_start: 0.6935 (pm20) cc_final: 0.6507 (pm20) REVERT: E 583 MET cc_start: 0.8673 (mtp) cc_final: 0.8428 (mtp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3250 time to fit residues: 88.5021 Evaluate side-chains 186 residues out of total 1167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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: 0.5980 chunk 100 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 0.1980 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 184 GLN ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.193841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.164990 restraints weight = 24914.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.168999 restraints weight = 16442.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.171832 restraints weight = 11888.310| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4414 r_free = 0.4414 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 = 0.4412 r_free = 0.4412 target_work(ls_wunit_k1) = 0.171 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4412 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.5258 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= 0.184 Angle : 0.678 12.983 16547 Z= 0.351 Chirality : 0.045 0.237 1896 Planarity : 0.004 0.053 1892 Dihedral : 19.374 166.580 2087 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.70 % Favored : 90.07 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -2.51 (0.22), residues: 1319 helix: -0.92 (0.30), residues: 296 sheet: -0.82 (0.29), residues: 319 loop : -2.47 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 431 HIS 0.003 0.001 HIS A 39 PHE 0.020 0.002 PHE C 128 TYR 0.018 0.001 TYR E 343 ARG 0.004 0.000 ARG C 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2793.44 seconds wall clock time: 58 minutes 48.29 seconds (3528.29 seconds total)