Starting phenix.real_space_refine on Wed Feb 14 09:21:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9y_33085/02_2024/7x9y_33085.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9y_33085/02_2024/7x9y_33085.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9y_33085/02_2024/7x9y_33085.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9y_33085/02_2024/7x9y_33085.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9y_33085/02_2024/7x9y_33085.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x9y_33085/02_2024/7x9y_33085.pdb" } resolution = 3.1 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= 0.033 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5744 2.51 5 N 1523 2.21 5 O 1649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 705": "OE1" <-> "OE2" Residue "B GLU 266": "OE1" <-> "OE2" Residue "R GLU 173": "OE1" <-> "OE2" Residue "R GLU 175": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8982 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1756 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 2412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2412 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "S" Number of atoms: 1763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1763 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain breaks: 1 Time building chain proxies: 5.13, per 1000 atoms: 0.57 Number of scatterers: 8982 At special positions: 0 Unit cell: (103.265, 130.44, 119.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1649 8.00 N 1523 7.00 C 5744 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 13 sheets defined 40.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 16 through 39 Processing helix chain 'A' and resid 51 through 438 removed outlier: 3.523A pdb=" N ILE A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 624 removed outlier: 4.263A pdb=" N ILE A 620 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N HIS A 621 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 639 removed outlier: 4.098A pdb=" N ASP A 639 " --> pdb=" O SER A 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 639' Processing helix chain 'A' and resid 649 through 663 Processing helix chain 'A' and resid 664 through 668 Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.991A pdb=" N LYS A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 694 Processing helix chain 'A' and resid 703 through 718 removed outlier: 3.655A pdb=" N ALA A 709 " --> pdb=" O GLU A 705 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 759 removed outlier: 3.672A pdb=" N PHE A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 31 removed outlier: 3.627A pdb=" N CYS B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.695A pdb=" N ILE B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 43 No H-bonds generated for 'chain 'B' and resid 41 through 43' Processing helix chain 'G' and resid 10 through 29 removed outlier: 3.944A pdb=" N ILE G 29 " --> pdb=" O MET G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 48 Processing helix chain 'G' and resid 49 through 52 removed outlier: 3.585A pdb=" N ASP G 52 " --> pdb=" O ALA G 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 52' Processing helix chain 'R' and resid 38 through 62 removed outlier: 3.613A pdb=" N SER R 42 " --> pdb=" O PRO R 38 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU R 43 " --> pdb=" O PRO R 39 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL R 54 " --> pdb=" O LEU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 96 Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 105 through 137 removed outlier: 3.637A pdb=" N TYR R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS R 114 " --> pdb=" O SER R 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.018A pdb=" N ARG R 143 " --> pdb=" O VAL R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 165 Processing helix chain 'R' and resid 165 through 170 Processing helix chain 'R' and resid 188 through 194 removed outlier: 3.508A pdb=" N VAL R 192 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR R 193 " --> pdb=" O ASP R 190 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER R 194 " --> pdb=" O THR R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 201 Processing helix chain 'R' and resid 201 through 206 removed outlier: 3.692A pdb=" N PHE R 206 " --> pdb=" O ARG R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 227 removed outlier: 3.892A pdb=" N GLY R 221 " --> pdb=" O ILE R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 264 removed outlier: 3.673A pdb=" N ALA R 237 " --> pdb=" O LYS R 233 " (cutoff:3.500A) Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 264 through 269 Processing helix chain 'R' and resid 272 through 292 Processing helix chain 'R' and resid 292 through 335 removed outlier: 3.590A pdb=" N MET R 296 " --> pdb=" O SER R 292 " (cutoff:3.500A) Proline residue: R 330 - end of helix Processing helix chain 'R' and resid 337 through 355 removed outlier: 3.746A pdb=" N ARG R 341 " --> pdb=" O GLY R 337 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.529A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'S' and resid 232 through 236 removed outlier: 3.831A pdb=" N VAL S 236 " --> pdb=" O ALA S 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 593 through 599 removed outlier: 6.985A pdb=" N LYS A 41 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE A 630 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU A 43 " --> pdb=" O ILE A 630 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N CYS A 632 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU A 45 " --> pdb=" O CYS A 632 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N ALA A 634 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE A 629 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N PHE A 675 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE A 631 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ASN A 677 " --> pdb=" O PHE A 631 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 633 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE A 672 " --> pdb=" O TYR A 728 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N HIS A 730 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LEU A 674 " --> pdb=" O HIS A 730 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 57 removed outlier: 6.441A pdb=" N THR B 53 " --> pdb=" O ASN B 346 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N ASN B 346 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 55 " --> pdb=" O ILE B 344 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS B 323 " --> pdb=" O GLY B 336 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 69 removed outlier: 3.749A pdb=" N ALA B 66 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 80 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LYS B 84 " --> pdb=" O SER B 80 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 85 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 98 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 87 " --> pdb=" O VAL B 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 106 through 111 removed outlier: 6.928A pdb=" N GLY B 121 " --> pdb=" O MET B 107 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N CYS B 109 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 119 " --> pdb=" O CYS B 109 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR B 111 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N TYR B 117 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE B 129 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG B 140 " --> pdb=" O ASN B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 158 removed outlier: 3.706A pdb=" N GLN B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE B 163 " --> pdb=" O TRP B 175 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N CYS B 172 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR B 185 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU B 174 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN B 181 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 198 removed outlier: 6.865A pdb=" N GLY B 208 " --> pdb=" O MET B 194 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 196 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 206 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU B 198 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU B 204 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 209 " --> pdb=" O SER B 213 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 226 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP B 218 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N CYS B 224 " --> pdb=" O ASP B 218 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 235 through 240 removed outlier: 3.804A pdb=" N ALA B 237 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET B 268 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP B 260 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLU B 266 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 284 removed outlier: 4.085A pdb=" N SER B 281 " --> pdb=" O GLY B 294 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 312 " --> pdb=" O VAL B 302 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.715A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.630A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 152 through 154 removed outlier: 3.552A pdb=" N VAL S 167 " --> pdb=" O ILE S 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 158 through 160 removed outlier: 3.573A pdb=" N GLU S 258 " --> pdb=" O VAL S 159 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL S 238 " --> pdb=" O GLN S 191 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU S 186 " --> pdb=" O TYR S 202 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR S 202 " --> pdb=" O LEU S 186 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N TRP S 188 " --> pdb=" O LEU S 200 " (cutoff:3.500A) 426 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.84 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1482 1.32 - 1.45: 2551 1.45 - 1.57: 5050 1.57 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 9180 Sorted by residual: bond pdb=" CA LEU B 196 " pdb=" C LEU B 196 " ideal model delta sigma weight residual 1.524 1.455 0.069 1.23e-02 6.61e+03 3.13e+01 bond pdb=" CA LEU B 196 " pdb=" CB LEU B 196 " ideal model delta sigma weight residual 1.533 1.471 0.062 1.51e-02 4.39e+03 1.69e+01 bond pdb=" C SER B 197 " pdb=" O SER B 197 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.25e-02 6.40e+03 9.74e+00 bond pdb=" CA SER B 197 " pdb=" CB SER B 197 " ideal model delta sigma weight residual 1.533 1.478 0.056 1.89e-02 2.80e+03 8.64e+00 bond pdb=" N LEU B 196 " pdb=" CA LEU B 196 " ideal model delta sigma weight residual 1.455 1.425 0.030 1.25e-02 6.40e+03 5.69e+00 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.21: 242 107.21 - 113.92: 5153 113.92 - 120.62: 3700 120.62 - 127.33: 3239 127.33 - 134.03: 95 Bond angle restraints: 12429 Sorted by residual: angle pdb=" N SER B 195 " pdb=" CA SER B 195 " pdb=" C SER B 195 " ideal model delta sigma weight residual 109.24 118.96 -9.72 1.67e+00 3.59e-01 3.39e+01 angle pdb=" C LEU B 196 " pdb=" CA LEU B 196 " pdb=" CB LEU B 196 " ideal model delta sigma weight residual 110.36 100.98 9.38 1.78e+00 3.16e-01 2.78e+01 angle pdb=" N VAL R 136 " pdb=" CA VAL R 136 " pdb=" C VAL R 136 " ideal model delta sigma weight residual 112.96 109.69 3.27 1.00e+00 1.00e+00 1.07e+01 angle pdb=" CA SER B 197 " pdb=" C SER B 197 " pdb=" N LEU B 198 " ideal model delta sigma weight residual 116.38 120.61 -4.23 1.35e+00 5.49e-01 9.82e+00 angle pdb=" C SER B 197 " pdb=" N LEU B 198 " pdb=" CA LEU B 198 " ideal model delta sigma weight residual 122.64 118.09 4.55 1.70e+00 3.46e-01 7.18e+00 ... (remaining 12424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 4939 16.62 - 33.25: 381 33.25 - 49.87: 76 49.87 - 66.50: 18 66.50 - 83.12: 4 Dihedral angle restraints: 5418 sinusoidal: 2113 harmonic: 3305 Sorted by residual: dihedral pdb=" C LEU B 196 " pdb=" N LEU B 196 " pdb=" CA LEU B 196 " pdb=" CB LEU B 196 " ideal model delta harmonic sigma weight residual -122.60 -109.01 -13.59 0 2.50e+00 1.60e-01 2.96e+01 dihedral pdb=" CA TYR S 202 " pdb=" C TYR S 202 " pdb=" N ARG S 203 " pdb=" CA ARG S 203 " ideal model delta harmonic sigma weight residual 180.00 162.22 17.78 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ARG S 203 " pdb=" C ARG S 203 " pdb=" N MET S 204 " pdb=" CA MET S 204 " ideal model delta harmonic sigma weight residual 180.00 162.55 17.45 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 875 0.027 - 0.055: 347 0.055 - 0.082: 98 0.082 - 0.110: 54 0.110 - 0.137: 32 Chirality restraints: 1406 Sorted by residual: chirality pdb=" CA MET B 268 " pdb=" N MET B 268 " pdb=" C MET B 268 " pdb=" CB MET B 268 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA VAL S 2 " pdb=" N VAL S 2 " pdb=" C VAL S 2 " pdb=" CB VAL S 2 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.90e-01 ... (remaining 1403 not shown) Planarity restraints: 1561 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR S 162 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO S 163 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO S 163 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 163 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 38 " -0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO R 39 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 39 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 39 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 58 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO G 59 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO G 59 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 59 " -0.021 5.00e-02 4.00e+02 ... (remaining 1558 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 41 2.53 - 3.12: 6946 3.12 - 3.71: 13456 3.71 - 4.31: 18599 4.31 - 4.90: 32006 Nonbonded interactions: 71048 Sorted by model distance: nonbonded pdb=" O LYS S 43 " pdb=" OH TYR S 240 " model vdw 1.932 2.440 nonbonded pdb=" O SER R 231 " pdb=" NZ LYS R 234 " model vdw 2.124 2.520 nonbonded pdb=" OG SER R 79 " pdb=" OG SER R 119 " model vdw 2.147 2.440 nonbonded pdb=" OG SER B 285 " pdb=" OD2 ASP G 52 " model vdw 2.163 2.440 nonbonded pdb=" O THR S 63 " pdb=" NH2 ARG S 67 " model vdw 2.177 2.520 ... (remaining 71043 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.420 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: 2.090 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.630 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 0.069 9180 Z= 0.173 Angle : 0.487 9.721 12429 Z= 0.277 Chirality : 0.038 0.137 1406 Planarity : 0.003 0.054 1561 Dihedral : 12.624 83.122 3288 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.31 % Allowed : 0.31 % Favored : 99.39 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.33 % 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: 2.03 (0.27), residues: 1121 helix: 2.91 (0.28), residues: 374 sheet: 1.42 (0.32), residues: 277 loop : 0.01 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 99 HIS 0.003 0.000 HIS B 231 PHE 0.010 0.001 PHE R 340 TYR 0.012 0.001 TYR A 704 ARG 0.009 0.001 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 324 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.7716 (mttm) cc_final: 0.7492 (ttmm) REVERT: A 599 PHE cc_start: 0.8221 (t80) cc_final: 0.7978 (t80) REVERT: A 712 GLN cc_start: 0.7735 (tm130) cc_final: 0.7011 (tm-30) REVERT: A 714 GLN cc_start: 0.7753 (tp-100) cc_final: 0.7372 (tp-100) REVERT: A 717 ASP cc_start: 0.7243 (m-30) cc_final: 0.6700 (m-30) REVERT: A 757 LYS cc_start: 0.8275 (mttp) cc_final: 0.7937 (mttp) REVERT: B 18 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 52 ARG cc_start: 0.7119 (mpt90) cc_final: 0.6806 (mpt90) REVERT: B 124 ASP cc_start: 0.6833 (p0) cc_final: 0.6379 (p0) REVERT: B 143 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7613 (mmm-85) REVERT: B 154 CYS cc_start: 0.7211 (t) cc_final: 0.6865 (t) REVERT: B 234 ASP cc_start: 0.7114 (m-30) cc_final: 0.6653 (m-30) REVERT: B 297 ASP cc_start: 0.6717 (t0) cc_final: 0.6122 (t0) REVERT: B 331 MET cc_start: 0.7178 (tpp) cc_final: 0.6945 (tpp) REVERT: G 25 MET cc_start: 0.7534 (tpp) cc_final: 0.7062 (tpp) REVERT: R 70 ASN cc_start: 0.7397 (m110) cc_final: 0.7194 (m110) REVERT: R 84 LEU cc_start: 0.7609 (pp) cc_final: 0.7406 (pp) REVERT: R 152 ILE cc_start: 0.8093 (mt) cc_final: 0.7854 (mt) REVERT: R 203 MET cc_start: 0.4847 (mtp) cc_final: 0.4250 (mtp) REVERT: R 279 LEU cc_start: 0.8381 (tp) cc_final: 0.8162 (tp) REVERT: R 284 LEU cc_start: 0.7741 (mp) cc_final: 0.7398 (mp) REVERT: S 13 GLN cc_start: 0.8290 (mm-40) cc_final: 0.8038 (mm-40) outliers start: 3 outliers final: 1 residues processed: 324 average time/residue: 0.2685 time to fit residues: 112.6393 Evaluate side-chains 310 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 196 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 HIS B 97 HIS R 114 HIS R 349 HIS ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9180 Z= 0.244 Angle : 0.575 8.021 12429 Z= 0.302 Chirality : 0.043 0.214 1406 Planarity : 0.004 0.053 1561 Dihedral : 4.192 44.414 1238 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.84 % Allowed : 10.51 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.51 (0.26), residues: 1121 helix: 2.09 (0.27), residues: 399 sheet: 1.41 (0.31), residues: 280 loop : -0.27 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 99 HIS 0.006 0.001 HIS S 35 PHE 0.028 0.002 PHE R 348 TYR 0.017 0.002 TYR R 219 ARG 0.008 0.001 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 314 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7299 (m-30) cc_final: 0.7064 (m-30) REVERT: A 599 PHE cc_start: 0.8185 (t80) cc_final: 0.7911 (t80) REVERT: A 705 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 716 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7594 (mt-10) REVERT: A 720 LYS cc_start: 0.8267 (mmtp) cc_final: 0.7957 (mppt) REVERT: A 749 ASP cc_start: 0.7818 (t0) cc_final: 0.7423 (t0) REVERT: B 18 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8290 (mm-30) REVERT: B 19 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7609 (pp30) REVERT: B 52 ARG cc_start: 0.7142 (mpt90) cc_final: 0.6881 (mpt180) REVERT: B 84 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7746 (mttp) REVERT: B 124 ASP cc_start: 0.6967 (p0) cc_final: 0.6565 (p0) REVERT: B 218 ASP cc_start: 0.6920 (t0) cc_final: 0.6710 (t70) REVERT: B 234 ASP cc_start: 0.7264 (m-30) cc_final: 0.6837 (m-30) REVERT: B 260 ASP cc_start: 0.7000 (t70) cc_final: 0.6791 (t70) REVERT: G 25 MET cc_start: 0.7536 (tpp) cc_final: 0.7056 (tpp) REVERT: R 151 VAL cc_start: 0.8184 (t) cc_final: 0.7910 (m) REVERT: R 152 ILE cc_start: 0.8222 (mt) cc_final: 0.7960 (mt) REVERT: R 203 MET cc_start: 0.4894 (mtp) cc_final: 0.4376 (mtp) REVERT: R 219 TYR cc_start: 0.7691 (m-10) cc_final: 0.7490 (m-10) REVERT: R 279 LEU cc_start: 0.8518 (tp) cc_final: 0.8288 (tp) REVERT: S 13 GLN cc_start: 0.8260 (mm-40) cc_final: 0.8006 (mm-40) REVERT: S 87 ARG cc_start: 0.7909 (mtm-85) cc_final: 0.7045 (mtm-85) REVERT: S 168 SER cc_start: 0.7906 (m) cc_final: 0.7654 (t) REVERT: S 240 TYR cc_start: 0.7509 (m-80) cc_final: 0.6858 (m-80) outliers start: 18 outliers final: 13 residues processed: 319 average time/residue: 0.2321 time to fit residues: 98.4767 Evaluate side-chains 309 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 295 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 LEU Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 216 SER Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 81 GLN B 97 HIS ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9180 Z= 0.253 Angle : 0.554 7.597 12429 Z= 0.291 Chirality : 0.044 0.224 1406 Planarity : 0.004 0.055 1561 Dihedral : 3.999 21.132 1236 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.57 % Allowed : 13.27 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.44 (0.26), residues: 1121 helix: 2.10 (0.27), residues: 393 sheet: 1.34 (0.31), residues: 286 loop : -0.34 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 88 HIS 0.006 0.001 HIS S 35 PHE 0.019 0.002 PHE R 348 TYR 0.012 0.001 TYR B 111 ARG 0.006 0.000 ARG S 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 307 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8190 (t80) cc_final: 0.7886 (t80) REVERT: A 605 LYS cc_start: 0.8262 (ttmt) cc_final: 0.8009 (ttmt) REVERT: A 680 ASP cc_start: 0.8269 (p0) cc_final: 0.8012 (p0) REVERT: A 684 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 705 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 716 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7631 (mt-10) REVERT: A 720 LYS cc_start: 0.8290 (mmtp) cc_final: 0.7971 (mttp) REVERT: A 749 ASP cc_start: 0.7816 (t0) cc_final: 0.7323 (t0) REVERT: B 18 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8305 (mm-30) REVERT: B 19 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7620 (pp30) REVERT: B 48 ARG cc_start: 0.7108 (ttm-80) cc_final: 0.6813 (ttm-80) REVERT: B 82 ASP cc_start: 0.7159 (m-30) cc_final: 0.6951 (m-30) REVERT: B 124 ASP cc_start: 0.7015 (p0) cc_final: 0.6566 (p0) REVERT: B 234 ASP cc_start: 0.7283 (m-30) cc_final: 0.6933 (m-30) REVERT: B 260 ASP cc_start: 0.7067 (t70) cc_final: 0.6852 (t70) REVERT: B 275 ILE cc_start: 0.8113 (mt) cc_final: 0.7764 (tp) REVERT: B 304 ASP cc_start: 0.7670 (t0) cc_final: 0.7158 (t70) REVERT: G 25 MET cc_start: 0.7586 (tpp) cc_final: 0.7098 (tpp) REVERT: R 152 ILE cc_start: 0.8241 (mt) cc_final: 0.7969 (mt) REVERT: R 203 MET cc_start: 0.4878 (mtp) cc_final: 0.4345 (mtp) REVERT: R 279 LEU cc_start: 0.8514 (tp) cc_final: 0.8274 (tp) REVERT: S 20 LEU cc_start: 0.8566 (mt) cc_final: 0.8331 (mt) REVERT: S 87 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7486 (mtm-85) REVERT: S 240 TYR cc_start: 0.7533 (m-80) cc_final: 0.6812 (m-80) outliers start: 35 outliers final: 23 residues processed: 315 average time/residue: 0.2837 time to fit residues: 117.9226 Evaluate side-chains 323 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 299 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 90 TRP Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 289 ILE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.0270 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9180 Z= 0.175 Angle : 0.530 7.350 12429 Z= 0.275 Chirality : 0.042 0.290 1406 Planarity : 0.004 0.056 1561 Dihedral : 3.919 20.813 1236 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.67 % Allowed : 15.92 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.46 (0.26), residues: 1121 helix: 2.13 (0.27), residues: 393 sheet: 1.23 (0.30), residues: 289 loop : -0.27 (0.32), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 345 HIS 0.004 0.001 HIS B 60 PHE 0.015 0.001 PHE R 348 TYR 0.010 0.001 TYR S 202 ARG 0.006 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 306 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8166 (t80) cc_final: 0.7838 (t80) REVERT: A 605 LYS cc_start: 0.8243 (ttmt) cc_final: 0.8032 (ttmt) REVERT: A 680 ASP cc_start: 0.8219 (p0) cc_final: 0.7963 (p0) REVERT: A 684 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 705 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 716 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7669 (mt-10) REVERT: A 717 ASP cc_start: 0.7718 (t0) cc_final: 0.7318 (t0) REVERT: A 720 LYS cc_start: 0.8261 (mmtp) cc_final: 0.7929 (mttp) REVERT: A 749 ASP cc_start: 0.7873 (t0) cc_final: 0.7343 (t0) REVERT: B 18 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 19 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7557 (pp30) REVERT: B 48 ARG cc_start: 0.7087 (ttm-80) cc_final: 0.6778 (ttm-80) REVERT: B 52 ARG cc_start: 0.7096 (mpt180) cc_final: 0.6686 (mpt180) REVERT: B 82 ASP cc_start: 0.7208 (m-30) cc_final: 0.6998 (m-30) REVERT: B 84 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7704 (mttp) REVERT: B 124 ASP cc_start: 0.7015 (p0) cc_final: 0.6588 (p0) REVERT: B 190 THR cc_start: 0.8353 (p) cc_final: 0.7904 (p) REVERT: B 197 SER cc_start: 0.8071 (t) cc_final: 0.7319 (p) REVERT: B 234 ASP cc_start: 0.7247 (m-30) cc_final: 0.6878 (m-30) REVERT: B 267 LEU cc_start: 0.8550 (mm) cc_final: 0.8306 (mm) REVERT: B 275 ILE cc_start: 0.8108 (mt) cc_final: 0.7864 (tp) REVERT: B 304 ASP cc_start: 0.7631 (t0) cc_final: 0.7301 (t70) REVERT: G 25 MET cc_start: 0.7579 (tpp) cc_final: 0.7103 (tpp) REVERT: G 41 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8613 (mp) REVERT: R 152 ILE cc_start: 0.8206 (mt) cc_final: 0.7960 (mt) REVERT: R 203 MET cc_start: 0.4899 (mtp) cc_final: 0.4388 (mtp) REVERT: R 247 VAL cc_start: 0.7726 (t) cc_final: 0.6655 (m) REVERT: R 279 LEU cc_start: 0.8506 (tp) cc_final: 0.8268 (tp) REVERT: S 20 LEU cc_start: 0.8561 (mt) cc_final: 0.8356 (mt) REVERT: S 29 PHE cc_start: 0.7815 (t80) cc_final: 0.7305 (t80) REVERT: S 87 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7606 (mtm-85) REVERT: S 240 TYR cc_start: 0.7547 (m-80) cc_final: 0.6759 (m-80) REVERT: S 243 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8230 (pp30) outliers start: 36 outliers final: 27 residues processed: 316 average time/residue: 0.2481 time to fit residues: 103.3331 Evaluate side-chains 329 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 299 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 90 TRP Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain S residue 243 GLN Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9180 Z= 0.209 Angle : 0.533 7.030 12429 Z= 0.279 Chirality : 0.042 0.295 1406 Planarity : 0.004 0.059 1561 Dihedral : 3.956 19.991 1236 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.39 % Allowed : 16.53 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.37 (0.26), residues: 1121 helix: 2.09 (0.27), residues: 393 sheet: 1.14 (0.30), residues: 293 loop : -0.33 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 345 HIS 0.005 0.001 HIS B 60 PHE 0.013 0.001 PHE R 348 TYR 0.027 0.001 TYR S 202 ARG 0.007 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 312 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8185 (t80) cc_final: 0.7817 (t80) REVERT: A 680 ASP cc_start: 0.8231 (p0) cc_final: 0.7957 (p0) REVERT: A 684 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 705 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7355 (mm-30) REVERT: A 716 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7680 (mt-10) REVERT: A 717 ASP cc_start: 0.7753 (t0) cc_final: 0.7346 (t0) REVERT: A 720 LYS cc_start: 0.8356 (mmtp) cc_final: 0.8043 (mttp) REVERT: A 749 ASP cc_start: 0.7857 (t0) cc_final: 0.7332 (t0) REVERT: B 18 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8331 (mm-30) REVERT: B 19 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7505 (pp30) REVERT: B 20 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.7900 (mm) REVERT: B 48 ARG cc_start: 0.7093 (ttm-80) cc_final: 0.6777 (ttm-80) REVERT: B 52 ARG cc_start: 0.7080 (mpt180) cc_final: 0.6716 (mpt180) REVERT: B 82 ASP cc_start: 0.7202 (m-30) cc_final: 0.6996 (m-30) REVERT: B 84 LYS cc_start: 0.8115 (mtpp) cc_final: 0.7864 (mttp) REVERT: B 124 ASP cc_start: 0.7014 (p0) cc_final: 0.6587 (p0) REVERT: B 190 THR cc_start: 0.8320 (p) cc_final: 0.8010 (p) REVERT: B 197 SER cc_start: 0.8119 (t) cc_final: 0.7350 (p) REVERT: B 218 ASP cc_start: 0.6732 (t70) cc_final: 0.6179 (p0) REVERT: B 234 ASP cc_start: 0.7231 (m-30) cc_final: 0.6839 (m-30) REVERT: B 257 ARG cc_start: 0.8213 (mtt180) cc_final: 0.7489 (mmm-85) REVERT: B 275 ILE cc_start: 0.8151 (mt) cc_final: 0.7830 (tp) REVERT: B 304 ASP cc_start: 0.7629 (t0) cc_final: 0.7303 (t70) REVERT: G 25 MET cc_start: 0.7579 (tpp) cc_final: 0.7099 (tpp) REVERT: G 41 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8625 (mp) REVERT: R 152 ILE cc_start: 0.8212 (mt) cc_final: 0.7978 (mt) REVERT: R 203 MET cc_start: 0.4863 (mtp) cc_final: 0.4324 (mtp) REVERT: R 212 LEU cc_start: 0.8136 (mt) cc_final: 0.7878 (mt) REVERT: R 279 LEU cc_start: 0.8539 (tp) cc_final: 0.8287 (tp) REVERT: R 341 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7535 (mtp85) REVERT: S 20 LEU cc_start: 0.8612 (mt) cc_final: 0.8376 (mt) REVERT: S 29 PHE cc_start: 0.7935 (t80) cc_final: 0.7328 (t80) REVERT: S 87 ARG cc_start: 0.7791 (mtm-85) cc_final: 0.7543 (mtm-85) REVERT: S 224 PHE cc_start: 0.7531 (m-10) cc_final: 0.6853 (m-10) REVERT: S 240 TYR cc_start: 0.7584 (m-80) cc_final: 0.6738 (m-80) outliers start: 43 outliers final: 31 residues processed: 326 average time/residue: 0.2317 time to fit residues: 100.8108 Evaluate side-chains 338 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 303 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 90 TRP Chi-restraints excluded: chain R residue 113 TYR Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9180 Z= 0.253 Angle : 0.569 7.112 12429 Z= 0.296 Chirality : 0.044 0.331 1406 Planarity : 0.004 0.058 1561 Dihedral : 4.111 22.376 1236 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.29 % Allowed : 17.96 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.27 (0.26), residues: 1121 helix: 2.01 (0.27), residues: 393 sheet: 1.00 (0.30), residues: 292 loop : -0.32 (0.32), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 345 HIS 0.006 0.001 HIS S 35 PHE 0.016 0.002 PHE B 186 TYR 0.035 0.002 TYR S 202 ARG 0.007 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 316 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8218 (t80) cc_final: 0.7801 (t80) REVERT: A 605 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7862 (mtmt) REVERT: A 664 ASN cc_start: 0.7682 (t0) cc_final: 0.7474 (t0) REVERT: A 680 ASP cc_start: 0.8228 (p0) cc_final: 0.7934 (p0) REVERT: A 684 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 705 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7368 (mm-30) REVERT: A 717 ASP cc_start: 0.7801 (t0) cc_final: 0.7403 (t0) REVERT: A 739 ASN cc_start: 0.7801 (m110) cc_final: 0.7584 (m110) REVERT: A 749 ASP cc_start: 0.7842 (t0) cc_final: 0.7313 (t0) REVERT: B 18 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8355 (mm-30) REVERT: B 19 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7525 (pp30) REVERT: B 20 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.7925 (mm) REVERT: B 25 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8052 (ttp80) REVERT: B 48 ARG cc_start: 0.7116 (ttm-80) cc_final: 0.6804 (ttm-80) REVERT: B 52 ARG cc_start: 0.7085 (mpt180) cc_final: 0.6712 (mpt180) REVERT: B 82 ASP cc_start: 0.7233 (m-30) cc_final: 0.7023 (m-30) REVERT: B 84 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7934 (mttp) REVERT: B 124 ASP cc_start: 0.7081 (p0) cc_final: 0.6656 (p0) REVERT: B 197 SER cc_start: 0.8210 (t) cc_final: 0.7461 (p) REVERT: B 218 ASP cc_start: 0.6797 (t70) cc_final: 0.6230 (p0) REVERT: B 223 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6711 (ttp) REVERT: B 234 ASP cc_start: 0.7202 (m-30) cc_final: 0.6788 (m-30) REVERT: B 257 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7630 (mmm-85) REVERT: B 304 ASP cc_start: 0.7596 (t0) cc_final: 0.7281 (t70) REVERT: G 25 MET cc_start: 0.7597 (tpp) cc_final: 0.7115 (tpp) REVERT: G 41 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8660 (mp) REVERT: R 152 ILE cc_start: 0.8220 (mt) cc_final: 0.7995 (mt) REVERT: R 203 MET cc_start: 0.4940 (mtp) cc_final: 0.4370 (mtp) REVERT: R 219 TYR cc_start: 0.8125 (m-10) cc_final: 0.7801 (m-80) REVERT: R 279 LEU cc_start: 0.8493 (tp) cc_final: 0.8250 (tp) REVERT: R 341 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7572 (mtp85) REVERT: S 20 LEU cc_start: 0.8673 (mt) cc_final: 0.8385 (mt) REVERT: S 224 PHE cc_start: 0.7538 (m-10) cc_final: 0.6806 (m-10) REVERT: S 240 TYR cc_start: 0.7593 (m-80) cc_final: 0.7209 (m-80) outliers start: 42 outliers final: 30 residues processed: 329 average time/residue: 0.2234 time to fit residues: 98.7736 Evaluate side-chains 345 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 310 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 665 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain R residue 71 ILE Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 225 THR Chi-restraints excluded: chain S residue 227 THR Chi-restraints excluded: chain S residue 255 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9180 Z= 0.189 Angle : 0.551 6.941 12429 Z= 0.287 Chirality : 0.043 0.277 1406 Planarity : 0.004 0.058 1561 Dihedral : 4.046 20.094 1236 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.78 % Allowed : 19.80 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.32 (0.26), residues: 1121 helix: 2.06 (0.27), residues: 393 sheet: 1.06 (0.30), residues: 279 loop : -0.28 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 252 HIS 0.005 0.001 HIS B 60 PHE 0.019 0.001 PHE S 251 TYR 0.032 0.001 TYR S 202 ARG 0.007 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 306 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 599 PHE cc_start: 0.8192 (t80) cc_final: 0.7800 (t80) REVERT: A 680 ASP cc_start: 0.8204 (p0) cc_final: 0.7899 (p0) REVERT: A 684 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 705 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 716 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7585 (mt-10) REVERT: A 717 ASP cc_start: 0.7780 (t0) cc_final: 0.7371 (t0) REVERT: A 749 ASP cc_start: 0.7833 (t0) cc_final: 0.7340 (t0) REVERT: B 18 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8347 (mm-30) REVERT: B 19 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7490 (pp30) REVERT: B 20 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7875 (mm) REVERT: B 48 ARG cc_start: 0.7092 (ttm-80) cc_final: 0.6794 (ttm-80) REVERT: B 52 ARG cc_start: 0.7067 (mpt180) cc_final: 0.6702 (mpt180) REVERT: B 82 ASP cc_start: 0.7225 (m-30) cc_final: 0.6999 (m-30) REVERT: B 84 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7839 (mttp) REVERT: B 120 CYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6349 (p) REVERT: B 124 ASP cc_start: 0.7063 (p0) cc_final: 0.6636 (p0) REVERT: B 197 SER cc_start: 0.8170 (t) cc_final: 0.7404 (p) REVERT: B 218 ASP cc_start: 0.6536 (t70) cc_final: 0.6063 (p0) REVERT: B 223 MET cc_start: 0.6921 (OUTLIER) cc_final: 0.6707 (ttp) REVERT: B 234 ASP cc_start: 0.7196 (m-30) cc_final: 0.6788 (m-30) REVERT: B 257 ARG cc_start: 0.8160 (mtt180) cc_final: 0.7667 (mmm-85) REVERT: B 267 LEU cc_start: 0.8542 (mm) cc_final: 0.8339 (mm) REVERT: B 304 ASP cc_start: 0.7577 (t0) cc_final: 0.7263 (t70) REVERT: G 25 MET cc_start: 0.7594 (tpp) cc_final: 0.7109 (tpp) REVERT: R 152 ILE cc_start: 0.8203 (mt) cc_final: 0.7984 (mt) REVERT: R 219 TYR cc_start: 0.8131 (m-10) cc_final: 0.7792 (m-80) REVERT: R 247 VAL cc_start: 0.7755 (t) cc_final: 0.6634 (m) REVERT: R 341 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7516 (mtp85) REVERT: S 20 LEU cc_start: 0.8628 (mt) cc_final: 0.8336 (mt) REVERT: S 50 TYR cc_start: 0.8174 (t80) cc_final: 0.7748 (t80) REVERT: S 87 ARG cc_start: 0.7506 (mtm-85) cc_final: 0.7107 (mtm-85) REVERT: S 93 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7305 (tpp) REVERT: S 187 TYR cc_start: 0.7804 (m-10) cc_final: 0.7285 (m-10) REVERT: S 224 PHE cc_start: 0.7394 (m-10) cc_final: 0.6684 (m-10) REVERT: S 240 TYR cc_start: 0.7607 (m-80) cc_final: 0.7192 (m-80) outliers start: 37 outliers final: 24 residues processed: 318 average time/residue: 0.2317 time to fit residues: 98.1917 Evaluate side-chains 328 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 298 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 245 ASN Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 225 THR Chi-restraints excluded: chain S residue 227 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9180 Z= 0.214 Angle : 0.568 7.170 12429 Z= 0.294 Chirality : 0.043 0.274 1406 Planarity : 0.004 0.058 1561 Dihedral : 4.071 19.921 1236 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.59 % Allowed : 18.88 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.27 (0.26), residues: 1121 helix: 2.03 (0.27), residues: 393 sheet: 0.99 (0.30), residues: 284 loop : -0.30 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 252 HIS 0.005 0.001 HIS B 60 PHE 0.022 0.002 PHE A 742 TYR 0.030 0.002 TYR S 202 ARG 0.006 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 307 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6983 (t0) REVERT: A 599 PHE cc_start: 0.8210 (t80) cc_final: 0.7779 (t80) REVERT: A 680 ASP cc_start: 0.8209 (p0) cc_final: 0.7914 (p0) REVERT: A 684 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7577 (mm-30) REVERT: A 705 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7375 (mm-30) REVERT: A 716 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7549 (mt-10) REVERT: A 717 ASP cc_start: 0.7790 (t0) cc_final: 0.7393 (t0) REVERT: A 749 ASP cc_start: 0.7845 (t0) cc_final: 0.7340 (t0) REVERT: B 18 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8354 (mm-30) REVERT: B 19 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7498 (pp30) REVERT: B 20 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.7877 (mm) REVERT: B 25 ARG cc_start: 0.8339 (ttp80) cc_final: 0.8047 (ttp80) REVERT: B 48 ARG cc_start: 0.7102 (ttm-80) cc_final: 0.6792 (ttm-80) REVERT: B 52 ARG cc_start: 0.7076 (mpt180) cc_final: 0.6708 (mpt180) REVERT: B 82 ASP cc_start: 0.7228 (m-30) cc_final: 0.6993 (m-30) REVERT: B 84 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7910 (mttp) REVERT: B 120 CYS cc_start: 0.6672 (OUTLIER) cc_final: 0.6390 (p) REVERT: B 124 ASP cc_start: 0.7066 (p0) cc_final: 0.6642 (p0) REVERT: B 141 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8473 (m) REVERT: B 197 SER cc_start: 0.8193 (t) cc_final: 0.7438 (p) REVERT: B 218 ASP cc_start: 0.6549 (t70) cc_final: 0.6080 (p0) REVERT: B 223 MET cc_start: 0.6920 (OUTLIER) cc_final: 0.6674 (ttp) REVERT: B 234 ASP cc_start: 0.7213 (m-30) cc_final: 0.6796 (m-30) REVERT: B 257 ARG cc_start: 0.8140 (mtt180) cc_final: 0.7661 (mmm-85) REVERT: B 267 LEU cc_start: 0.8553 (mm) cc_final: 0.8327 (mm) REVERT: B 304 ASP cc_start: 0.7583 (t0) cc_final: 0.7270 (t70) REVERT: G 25 MET cc_start: 0.7605 (tpp) cc_final: 0.7115 (tpp) REVERT: R 127 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7516 (mt) REVERT: R 152 ILE cc_start: 0.8199 (mt) cc_final: 0.7981 (mt) REVERT: R 203 MET cc_start: 0.4986 (mtp) cc_final: 0.4464 (mtp) REVERT: R 219 TYR cc_start: 0.8146 (m-10) cc_final: 0.7806 (m-80) REVERT: R 341 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7530 (mtp85) REVERT: S 20 LEU cc_start: 0.8618 (mt) cc_final: 0.8335 (mt) REVERT: S 29 PHE cc_start: 0.8440 (t80) cc_final: 0.7584 (t80) REVERT: S 50 TYR cc_start: 0.8186 (t80) cc_final: 0.7737 (t80) REVERT: S 187 TYR cc_start: 0.7889 (m-10) cc_final: 0.7567 (m-10) REVERT: S 240 TYR cc_start: 0.7663 (m-80) cc_final: 0.7220 (m-80) outliers start: 45 outliers final: 27 residues processed: 324 average time/residue: 0.2348 time to fit residues: 101.0062 Evaluate side-chains 337 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 302 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 120 CYS Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 156 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 225 THR Chi-restraints excluded: chain S residue 227 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 4.9990 chunk 59 optimal weight: 0.0870 chunk 43 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 63 optimal weight: 0.6980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 81 GLN R 297 ASN ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9180 Z= 0.167 Angle : 0.550 7.539 12429 Z= 0.285 Chirality : 0.042 0.238 1406 Planarity : 0.004 0.057 1561 Dihedral : 3.997 17.504 1236 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.49 % Allowed : 19.80 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.30 (0.26), residues: 1121 helix: 2.07 (0.27), residues: 395 sheet: 0.95 (0.30), residues: 293 loop : -0.29 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 252 HIS 0.005 0.001 HIS B 60 PHE 0.016 0.001 PHE A 742 TYR 0.029 0.001 TYR S 202 ARG 0.008 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 309 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6914 (t0) REVERT: A 599 PHE cc_start: 0.8176 (t80) cc_final: 0.7711 (t80) REVERT: A 607 PHE cc_start: 0.7789 (m-80) cc_final: 0.7555 (m-10) REVERT: A 680 ASP cc_start: 0.8204 (p0) cc_final: 0.7893 (p0) REVERT: A 684 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 705 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7309 (mm-30) REVERT: A 716 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7465 (mt-10) REVERT: A 717 ASP cc_start: 0.7761 (t0) cc_final: 0.7358 (t0) REVERT: A 725 LYS cc_start: 0.8066 (OUTLIER) cc_final: 0.7783 (tttm) REVERT: A 729 THR cc_start: 0.7966 (p) cc_final: 0.7744 (p) REVERT: A 749 ASP cc_start: 0.7846 (t0) cc_final: 0.7315 (t0) REVERT: B 18 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8335 (mm-30) REVERT: B 19 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7481 (pp30) REVERT: B 20 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7879 (mm) REVERT: B 25 ARG cc_start: 0.8352 (ttp80) cc_final: 0.8073 (ttp80) REVERT: B 48 ARG cc_start: 0.7097 (ttm-80) cc_final: 0.6797 (ttm-80) REVERT: B 52 ARG cc_start: 0.7068 (mpt180) cc_final: 0.6692 (mpt180) REVERT: B 124 ASP cc_start: 0.7003 (p0) cc_final: 0.6574 (p0) REVERT: B 197 SER cc_start: 0.8085 (t) cc_final: 0.7423 (p) REVERT: B 218 ASP cc_start: 0.6551 (t70) cc_final: 0.6185 (p0) REVERT: B 223 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6656 (ttp) REVERT: B 234 ASP cc_start: 0.7232 (m-30) cc_final: 0.6812 (m-30) REVERT: B 238 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8156 (tp) REVERT: B 257 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7666 (mmm-85) REVERT: B 260 ASP cc_start: 0.7108 (t70) cc_final: 0.6764 (t70) REVERT: B 304 ASP cc_start: 0.7568 (t0) cc_final: 0.7264 (t70) REVERT: G 25 MET cc_start: 0.7598 (tpp) cc_final: 0.7101 (tpp) REVERT: R 127 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7471 (mt) REVERT: R 152 ILE cc_start: 0.8168 (mt) cc_final: 0.7926 (mt) REVERT: R 247 VAL cc_start: 0.7717 (t) cc_final: 0.6576 (m) REVERT: R 251 PHE cc_start: 0.7456 (m-10) cc_final: 0.7129 (m-10) REVERT: R 341 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7463 (mtp85) REVERT: S 20 LEU cc_start: 0.8594 (mt) cc_final: 0.8352 (mt) REVERT: S 29 PHE cc_start: 0.8478 (t80) cc_final: 0.7679 (t80) REVERT: S 50 TYR cc_start: 0.8115 (t80) cc_final: 0.7698 (t80) REVERT: S 111 TRP cc_start: 0.8764 (m-10) cc_final: 0.8421 (m-10) REVERT: S 187 TYR cc_start: 0.7884 (m-10) cc_final: 0.7644 (m-10) REVERT: S 240 TYR cc_start: 0.7637 (m-80) cc_final: 0.7017 (m-80) REVERT: S 257 LEU cc_start: 0.7608 (mm) cc_final: 0.7358 (mt) outliers start: 44 outliers final: 25 residues processed: 322 average time/residue: 0.2332 time to fit residues: 99.5591 Evaluate side-chains 338 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 305 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 225 THR Chi-restraints excluded: chain S residue 227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.0040 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN B 81 GLN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9180 Z= 0.195 Angle : 0.563 7.437 12429 Z= 0.291 Chirality : 0.043 0.275 1406 Planarity : 0.004 0.059 1561 Dihedral : 4.023 17.112 1236 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.47 % Allowed : 20.71 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.29 (0.26), residues: 1121 helix: 2.06 (0.27), residues: 394 sheet: 0.90 (0.30), residues: 298 loop : -0.27 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 252 HIS 0.006 0.001 HIS B 60 PHE 0.019 0.002 PHE A 742 TYR 0.027 0.001 TYR S 202 ARG 0.009 0.000 ARG S 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 305 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7093 (t0) REVERT: A 599 PHE cc_start: 0.8198 (t80) cc_final: 0.7742 (t80) REVERT: A 680 ASP cc_start: 0.8210 (p0) cc_final: 0.7898 (p0) REVERT: A 684 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 705 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7341 (mm-30) REVERT: A 716 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7473 (mt-10) REVERT: A 717 ASP cc_start: 0.7774 (t0) cc_final: 0.7365 (t0) REVERT: A 725 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7776 (tttm) REVERT: A 729 THR cc_start: 0.7976 (p) cc_final: 0.7766 (p) REVERT: A 749 ASP cc_start: 0.7860 (t0) cc_final: 0.7318 (t0) REVERT: B 19 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7492 (pp30) REVERT: B 20 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7865 (mm) REVERT: B 25 ARG cc_start: 0.8368 (ttp80) cc_final: 0.8081 (ttp80) REVERT: B 48 ARG cc_start: 0.7058 (ttm-80) cc_final: 0.6795 (ttm-80) REVERT: B 52 ARG cc_start: 0.7074 (mpt180) cc_final: 0.6739 (mpt180) REVERT: B 124 ASP cc_start: 0.7028 (p0) cc_final: 0.6620 (p0) REVERT: B 165 THR cc_start: 0.8284 (m) cc_final: 0.7928 (p) REVERT: B 197 SER cc_start: 0.8066 (t) cc_final: 0.7441 (p) REVERT: B 218 ASP cc_start: 0.6710 (t70) cc_final: 0.6298 (p0) REVERT: B 220 ARG cc_start: 0.7459 (mtt180) cc_final: 0.7247 (mtt180) REVERT: B 223 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.6699 (ttp) REVERT: B 234 ASP cc_start: 0.7249 (m-30) cc_final: 0.6827 (m-30) REVERT: B 238 ILE cc_start: 0.8462 (mm) cc_final: 0.8166 (tp) REVERT: B 257 ARG cc_start: 0.8116 (mtt180) cc_final: 0.7678 (mmm-85) REVERT: B 260 ASP cc_start: 0.7123 (t70) cc_final: 0.6799 (t70) REVERT: B 304 ASP cc_start: 0.7584 (t0) cc_final: 0.7276 (t70) REVERT: G 25 MET cc_start: 0.7608 (tpp) cc_final: 0.7115 (tpp) REVERT: R 127 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7673 (mt) REVERT: R 152 ILE cc_start: 0.8198 (mt) cc_final: 0.7984 (mt) REVERT: R 203 MET cc_start: 0.4972 (mtp) cc_final: 0.4459 (mtp) REVERT: R 219 TYR cc_start: 0.8171 (m-10) cc_final: 0.7820 (m-80) REVERT: R 341 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7549 (mtp85) REVERT: S 20 LEU cc_start: 0.8621 (mt) cc_final: 0.8353 (mt) REVERT: S 29 PHE cc_start: 0.8482 (t80) cc_final: 0.7808 (t80) REVERT: S 111 TRP cc_start: 0.8772 (m-10) cc_final: 0.8392 (m-10) REVERT: S 240 TYR cc_start: 0.7672 (m-80) cc_final: 0.7171 (m-80) REVERT: S 257 LEU cc_start: 0.7633 (mm) cc_final: 0.7375 (mt) outliers start: 34 outliers final: 24 residues processed: 316 average time/residue: 0.2390 time to fit residues: 100.2609 Evaluate side-chains 333 residues out of total 980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 302 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 32 ASP Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 618 LYS Chi-restraints excluded: chain A residue 725 LYS Chi-restraints excluded: chain A residue 758 ASP Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 140 ARG Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 223 MET Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 265 GLN Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 222 ILE Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 341 ARG Chi-restraints excluded: chain S residue 37 VAL Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 190 LEU Chi-restraints excluded: chain S residue 222 THR Chi-restraints excluded: chain S residue 225 THR Chi-restraints excluded: chain S residue 227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN ** R 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.144512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121903 restraints weight = 14001.077| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.66 r_work: 0.3512 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9180 Z= 0.193 Angle : 0.568 7.641 12429 Z= 0.293 Chirality : 0.043 0.271 1406 Planarity : 0.004 0.058 1561 Dihedral : 4.040 18.335 1236 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.16 % Allowed : 21.33 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.30 (0.26), residues: 1121 helix: 2.10 (0.27), residues: 394 sheet: 0.89 (0.30), residues: 298 loop : -0.29 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 252 HIS 0.006 0.001 HIS B 60 PHE 0.024 0.002 PHE R 348 TYR 0.027 0.001 TYR S 202 ARG 0.007 0.000 ARG S 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2603.98 seconds wall clock time: 47 minutes 45.65 seconds (2865.65 seconds total)